Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 19:51:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9u_24937/04_2023/7s9u_24937.pdb" } resolution = 3.2 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= 0.003 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: 5 Type Number sf(0) Gaussians P 2436 5.49 5 S 52 5.16 5 C 33528 2.51 5 N 12812 2.21 5 O 19792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "N TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 19": "OD1" <-> "OD2" Residue "N ASP 23": "OD1" <-> "OD2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 45": "OE1" <-> "OE2" Residue "N PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "P ASP 10": "OD1" <-> "OD2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "P ASP 19": "OD1" <-> "OD2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P GLU 41": "OE1" <-> "OE2" Residue "P TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "R TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R ASP 37": "OD1" <-> "OD2" Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S ASP 65": "OD1" <-> "OD2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "T ASP 19": "OD1" <-> "OD2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 31": "OD1" <-> "OD2" Residue "T GLU 38": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "V ASP 23": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "V TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "b ARG 6": "NH1" <-> "NH2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68620 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 52346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2436, 52346 Classifications: {'RNA': 2436} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 126, 'rna3p_pur': 1181, 'rna3p_pyr': 879} Link IDs: {'rna2p': 376, 'rna3p': 2059} Chain breaks: 5 Chain: "C" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2052 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1354 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 973 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 1 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "V" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Time building chain proxies: 26.33, per 1000 atoms: 0.38 Number of scatterers: 68620 At special positions: 0 Unit cell: (206.91, 196.65, 206.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2436 15.00 O 19792 8.00 N 12812 7.00 C 33528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 33 " - pdb=" SG CYS b 46 " distance=2.04 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: 27.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 33 sheets defined 24.1% alpha, 17.7% beta 697 base pairs and 1236 stacking pairs defined. Time for finding SS restraints: 21.24 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' 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 197 through 202 removed outlier: 3.675A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.156A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.849A pdb=" N SER D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.681A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 31 through 44 removed outlier: 3.894A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE E 37 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.887A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.656A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.874A pdb=" N SER J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 4.206A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 72 Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.715A pdb=" N GLU J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 121 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 removed outlier: 3.694A pdb=" N SER K 116 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.529A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 removed outlier: 3.631A pdb=" N THR L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.672A pdb=" N LYS L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.002A pdb=" N LYS N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE N 25 " --> pdb=" O THR N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 52 removed outlier: 4.661A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS N 52 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 3.529A pdb=" N ARG N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 86 removed outlier: 3.610A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 90 Processing helix chain 'P' and resid 6 through 10 Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.699A pdb=" N LEU P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 4.026A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG Q 13 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.058A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 57 removed outlier: 4.387A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Q 38 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET Q 40 " --> pdb=" O ASN Q 36 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY Q 43 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN Q 52 " --> pdb=" O ARG Q 48 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 removed outlier: 3.773A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 86 removed outlier: 3.914A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 118 removed outlier: 3.944A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.264A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.853A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 removed outlier: 3.506A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 Processing helix chain 'T' and resid 19 through 23 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.812A pdb=" N LYS T 40 " --> pdb=" O LYS T 36 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP T 41 " --> pdb=" O THR T 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.883A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG Z 24 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 4.036A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 Processing helix chain 'Y' and resid 17 through 35 removed outlier: 3.714A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 61 removed outlier: 3.670A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 17 removed outlier: 3.890A pdb=" N VAL d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.641A pdb=" N GLY d 38 " --> pdb=" O ARG d 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.941A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.583A pdb=" N LEU C 165 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 7 removed outlier: 7.129A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.560A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP D 54 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N ASN D 33 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 120 removed outlier: 3.718A pdb=" N GLN D 120 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 13 through 17 removed outlier: 4.914A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.092A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AB2, first strand: chain 'J' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 24 removed outlier: 7.113A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.443A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.975A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE L 111 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 124 through 125 Processing sheet with id=AB7, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.309A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU N 104 " --> pdb=" O MET N 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 71 through 74 Processing sheet with id=AB9, first strand: chain 'P' and resid 71 through 74 removed outlier: 6.770A pdb=" N THR P 63 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE P 67 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLU P 47 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.623A pdb=" N GLY R 66 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 71 through 77 removed outlier: 4.042A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.673A pdb=" N LYS S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL S 107 " --> pdb=" O LYS S 4 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL S 6 " --> pdb=" O ILE S 105 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE S 105 " --> pdb=" O VAL S 6 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AC6, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.641A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 63 through 66 removed outlier: 3.648A pdb=" N GLY T 71 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 33 through 35 removed outlier: 6.708A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY U 21 " --> pdb=" O VAL U 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL U 9 " --> pdb=" O GLY U 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 40 through 45 Processing sheet with id=AD1, first strand: chain 'U' and resid 81 through 85 Processing sheet with id=AD2, first strand: chain 'V' and resid 30 through 31 removed outlier: 7.219A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE V 68 " --> pdb=" O GLY V 60 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'V' and resid 78 through 79 removed outlier: 3.573A pdb=" N LYS V 86 " --> pdb=" O GLU V 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AD6, first strand: chain 'b' and resid 27 through 29 400 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1775 hydrogen bonds 2952 hydrogen bond angles 0 basepair planarities 697 basepair parallelities 1236 stacking parallelities Total time for adding SS restraints: 89.37 Time building geometry restraints manager: 29.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6664 1.31 - 1.44: 34093 1.44 - 1.56: 29392 1.56 - 1.69: 4866 1.69 - 1.81: 97 Bond restraints: 75112 Sorted by residual: bond pdb=" CA ASN J 8 " pdb=" CB ASN J 8 " ideal model delta sigma weight residual 1.527 1.398 0.129 2.48e-02 1.63e+03 2.71e+01 bond pdb=" O3' G A 160 " pdb=" P A A 161 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.84e+01 bond pdb=" C LYS E 100 " pdb=" N LEU E 101 " ideal model delta sigma weight residual 1.333 1.236 0.096 2.74e-02 1.33e+03 1.24e+01 bond pdb=" O3' G A 26 " pdb=" P G A 27 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.13e+01 bond pdb=" O5' G A1512 " pdb=" C5' G A1512 " ideal model delta sigma weight residual 1.420 1.469 -0.049 1.50e-02 4.44e+03 1.08e+01 ... (remaining 75107 not shown) Histogram of bond angle deviations from ideal: 87.21 - 96.94: 1 96.94 - 106.67: 15816 106.67 - 116.40: 52377 116.40 - 126.13: 37409 126.13 - 135.86: 7921 Bond angle restraints: 113524 Sorted by residual: angle pdb=" C3' C A1511 " pdb=" O3' C A1511 " pdb=" P G A1512 " ideal model delta sigma weight residual 120.20 135.86 -15.66 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C3' G A 160 " pdb=" O3' G A 160 " pdb=" P A A 161 " ideal model delta sigma weight residual 120.20 133.25 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" O3' G A 839 " pdb=" C3' G A 839 " pdb=" C2' G A 839 " ideal model delta sigma weight residual 109.50 121.32 -11.82 1.50e+00 4.44e-01 6.21e+01 angle pdb=" N VAL Q 90 " pdb=" CA VAL Q 90 " pdb=" C VAL Q 90 " ideal model delta sigma weight residual 108.12 97.90 10.22 1.34e+00 5.57e-01 5.82e+01 angle pdb=" O3' A A 161 " pdb=" C3' A A 161 " pdb=" C2' A A 161 " ideal model delta sigma weight residual 113.70 102.44 11.26 1.50e+00 4.44e-01 5.63e+01 ... (remaining 113519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 37205 35.92 - 71.84: 2059 71.84 - 107.76: 170 107.76 - 143.67: 46 143.67 - 179.59: 31 Dihedral angle restraints: 39511 sinusoidal: 33602 harmonic: 5909 Sorted by residual: dihedral pdb=" O4' U A 892 " pdb=" C1' U A 892 " pdb=" N1 U A 892 " pdb=" C2 U A 892 " ideal model delta sinusoidal sigma weight residual -160.00 16.67 -176.67 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual -160.00 16.16 -176.16 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 857 " pdb=" C1' U A 857 " pdb=" N1 U A 857 " pdb=" C2 U A 857 " ideal model delta sinusoidal sigma weight residual 200.00 24.61 175.39 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 39508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 14037 0.131 - 0.261: 595 0.261 - 0.392: 33 0.392 - 0.523: 1 0.523 - 0.654: 2 Chirality restraints: 14668 Sorted by residual: chirality pdb=" C3' G A 839 " pdb=" C4' G A 839 " pdb=" O3' G A 839 " pdb=" C2' G A 839 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C3' U A1595 " pdb=" C4' U A1595 " pdb=" O3' U A1595 " pdb=" C2' U A1595 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C1' G A1712 " pdb=" O4' G A1712 " pdb=" C2' G A1712 " pdb=" N9 G A1712 " both_signs ideal model delta sigma weight residual False 2.46 1.99 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 14665 not shown) Planarity restraints: 5269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " -0.098 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO R 51 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A1245 " 0.065 2.00e-02 2.50e+03 2.84e-02 2.43e+01 pdb=" N9 G A1245 " -0.070 2.00e-02 2.50e+03 pdb=" C8 G A1245 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G A1245 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A1245 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A1245 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G A1245 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G A1245 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A1245 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A1245 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G A1245 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1245 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1026 " 0.051 2.00e-02 2.50e+03 2.39e-02 1.57e+01 pdb=" N9 A A1026 " -0.058 2.00e-02 2.50e+03 pdb=" C8 A A1026 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A1026 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A1026 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A A1026 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A1026 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A A1026 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A1026 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1026 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A1026 " -0.003 2.00e-02 2.50e+03 ... (remaining 5266 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 9 1.79 - 2.57: 851 2.57 - 3.35: 74418 3.35 - 4.12: 206527 4.12 - 4.90: 311777 Nonbonded interactions: 593582 Sorted by model distance: nonbonded pdb=" N2 G A2099 " pdb=" O2 C A2471 " model vdw 1.016 2.496 nonbonded pdb=" N7 G A2096 " pdb=" O6 G A2098 " model vdw 1.382 3.120 nonbonded pdb=" O2' G A 251 " pdb=" OP1 A A2461 " model vdw 1.568 2.440 nonbonded pdb=" N6 A A2351 " pdb=" N6 A A2362 " model vdw 1.625 3.200 nonbonded pdb=" O6 G A2328 " pdb=" N2 G A2347 " model vdw 1.625 2.520 ... (remaining 593577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.040 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 212.040 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 : 0.011 0.129 75112 Z= 0.652 Angle : 0.963 20.794 113524 Z= 0.509 Chirality : 0.058 0.654 14668 Planarity : 0.006 0.149 5269 Dihedral : 18.258 179.593 35712 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 15.23 % Favored : 84.33 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.14), residues: 2048 helix: -3.90 (0.15), residues: 435 sheet: -3.29 (0.21), residues: 440 loop : -3.67 (0.14), residues: 1173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 299 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 322 average time/residue: 0.7242 time to fit residues: 393.7513 Evaluate side-chains 271 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6421 time to fit residues: 24.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 8.9990 chunk 336 optimal weight: 40.0000 chunk 186 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 211 optimal weight: 40.0000 chunk 259 optimal weight: 6.9990 chunk 403 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS C 111 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 83 HIS R 101 ASN S 37 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 75112 Z= 0.225 Angle : 0.651 10.988 113524 Z= 0.336 Chirality : 0.038 0.311 14668 Planarity : 0.005 0.138 5269 Dihedral : 17.562 179.457 31508 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.20 % Favored : 91.55 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.16), residues: 2048 helix: -2.66 (0.21), residues: 440 sheet: -2.56 (0.24), residues: 400 loop : -3.02 (0.15), residues: 1208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 282 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 314 average time/residue: 0.6523 time to fit residues: 352.5402 Evaluate side-chains 296 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.689 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 0.5059 time to fit residues: 37.1367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 335 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 436 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 324 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN S 37 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 75112 Z= 0.219 Angle : 0.594 9.627 113524 Z= 0.309 Chirality : 0.036 0.272 14668 Planarity : 0.005 0.129 5269 Dihedral : 17.337 179.575 31508 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.69 % Favored : 91.21 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.17), residues: 2048 helix: -1.84 (0.23), residues: 459 sheet: -2.13 (0.25), residues: 384 loop : -2.66 (0.16), residues: 1205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 279 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 296 average time/residue: 0.6780 time to fit residues: 346.2325 Evaluate side-chains 277 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 258 time to evaluate : 3.785 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5776 time to fit residues: 23.4206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 192 optimal weight: 30.0000 chunk 271 optimal weight: 6.9990 chunk 405 optimal weight: 8.9990 chunk 429 optimal weight: 10.0000 chunk 211 optimal weight: 40.0000 chunk 384 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN S 37 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 75112 Z= 0.281 Angle : 0.617 9.437 113524 Z= 0.319 Chirality : 0.037 0.268 14668 Planarity : 0.005 0.126 5269 Dihedral : 17.346 179.348 31508 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.59 % Favored : 91.31 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.17), residues: 2048 helix: -1.40 (0.24), residues: 451 sheet: -2.15 (0.25), residues: 403 loop : -2.44 (0.16), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 292 average time/residue: 0.7164 time to fit residues: 361.0436 Evaluate side-chains 279 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5332 time to fit residues: 24.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.6980 chunk 243 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 177 optimal weight: 40.0000 chunk 366 optimal weight: 0.0870 chunk 296 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 80.0000 chunk 385 optimal weight: 7.9990 chunk 108 optimal weight: 60.0000 overall best weight: 4.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 75112 Z= 0.159 Angle : 0.554 9.712 113524 Z= 0.288 Chirality : 0.033 0.259 14668 Planarity : 0.004 0.121 5269 Dihedral : 17.139 178.501 31508 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 2048 helix: -0.83 (0.25), residues: 441 sheet: -1.78 (0.26), residues: 389 loop : -2.30 (0.16), residues: 1218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 265 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 275 average time/residue: 0.6782 time to fit residues: 321.0916 Evaluate side-chains 258 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 246 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5150 time to fit residues: 14.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 40.0000 chunk 386 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 105 optimal weight: 40.0000 chunk 429 optimal weight: 20.0000 chunk 356 optimal weight: 20.0000 chunk 198 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 75112 Z= 0.373 Angle : 0.659 9.184 113524 Z= 0.338 Chirality : 0.039 0.281 14668 Planarity : 0.005 0.122 5269 Dihedral : 17.341 178.671 31508 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.42 % Favored : 90.48 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.17), residues: 2048 helix: -0.96 (0.25), residues: 446 sheet: -2.01 (0.24), residues: 420 loop : -2.34 (0.16), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 277 average time/residue: 0.6931 time to fit residues: 326.7548 Evaluate side-chains 269 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 time to evaluate : 2.696 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5034 time to fit residues: 19.1998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 197 optimal weight: 50.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 75112 Z= 0.261 Angle : 0.602 9.475 113524 Z= 0.312 Chirality : 0.036 0.262 14668 Planarity : 0.005 0.119 5269 Dihedral : 17.228 178.670 31508 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.06 % Favored : 91.85 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.18), residues: 2048 helix: -0.72 (0.25), residues: 443 sheet: -1.88 (0.25), residues: 405 loop : -2.22 (0.16), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 258 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 271 average time/residue: 0.6950 time to fit residues: 320.8487 Evaluate side-chains 261 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4890 time to fit residues: 16.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 255 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 211 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 336 optimal weight: 40.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 75112 Z= 0.440 Angle : 0.706 8.989 113524 Z= 0.360 Chirality : 0.041 0.313 14668 Planarity : 0.005 0.121 5269 Dihedral : 17.449 179.601 31508 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.30 % Favored : 89.55 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.17), residues: 2048 helix: -0.81 (0.24), residues: 444 sheet: -1.97 (0.25), residues: 410 loop : -2.26 (0.17), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 275 average time/residue: 0.6868 time to fit residues: 323.2049 Evaluate side-chains 270 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5401 time to fit residues: 22.6263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 8.9990 chunk 409 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 313 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 360 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 397 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 75112 Z= 0.155 Angle : 0.568 9.724 113524 Z= 0.295 Chirality : 0.034 0.257 14668 Planarity : 0.004 0.117 5269 Dihedral : 17.128 178.538 31508 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.08 % Favored : 92.82 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 2048 helix: -0.46 (0.25), residues: 440 sheet: -1.76 (0.25), residues: 409 loop : -2.06 (0.17), residues: 1199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 264 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 267 average time/residue: 0.7179 time to fit residues: 327.9082 Evaluate side-chains 260 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4903 time to fit residues: 10.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 6.9990 chunk 421 optimal weight: 0.0470 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 50.0000 chunk 293 optimal weight: 20.0000 chunk 442 optimal weight: 0.1980 chunk 407 optimal weight: 0.6980 chunk 352 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 overall best weight: 1.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN U 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 75112 Z= 0.116 Angle : 0.528 10.252 113524 Z= 0.272 Chirality : 0.031 0.273 14668 Planarity : 0.004 0.113 5269 Dihedral : 16.832 179.641 31508 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.20 % Favored : 93.70 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.18), residues: 2048 helix: -0.12 (0.25), residues: 443 sheet: -1.50 (0.26), residues: 398 loop : -1.88 (0.17), residues: 1207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 290 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 292 average time/residue: 0.6817 time to fit residues: 339.4965 Evaluate side-chains 265 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4837 time to fit residues: 5.5133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 20.0000 chunk 375 optimal weight: 0.9990 chunk 107 optimal weight: 60.0000 chunk 324 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 147 optimal weight: 30.0000 chunk 362 optimal weight: 40.0000 chunk 44 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.033143 restraints weight = 414129.808| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.78 r_work: 0.2573 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.085 75112 Z= 0.390 Angle : 0.687 11.131 113524 Z= 0.350 Chirality : 0.039 0.299 14668 Planarity : 0.005 0.118 5269 Dihedral : 17.148 178.393 31508 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.84 % Favored : 91.06 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 2048 helix: -0.42 (0.25), residues: 449 sheet: -1.68 (0.24), residues: 428 loop : -2.01 (0.17), residues: 1171 =============================================================================== Job complete usr+sys time: 9886.31 seconds wall clock time: 177 minutes 54.71 seconds (10674.71 seconds total)