Starting phenix.real_space_refine (version: dev) on Thu Feb 23 05:44:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/02_2023/6pvk_20491.pdb" } resolution = 3.4 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= 0.002 sd= 0.017 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 Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P GLU 105": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "b GLU 35": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 60554 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 46617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2169, 46617 Classifications: {'RNA': 2169} Modifications used: {'rna2p_pur': 214, 'rna2p_pyr': 104, 'rna3p_pur': 1062, 'rna3p_pyr': 789} Link IDs: {'rna2p': 318, 'rna3p': 1850} Chain breaks: 13 Chain: "C" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1680 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1264 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1391 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "L" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 716 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "R" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 761 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 780 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 1 Chain: "T" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 684 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 2 Chain: "b" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 414 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Y" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 517 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "d" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 327 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 25.45, per 1000 atoms: 0.42 Number of scatterers: 60554 At special positions: 0 Unit cell: (207.089, 151.293, 223.184, 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 43 16.00 P 2169 15.00 O 17535 8.00 N 11276 7.00 C 29531 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: 27.46 Conformation dependent library (CDL) restraints added in 1.9 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 29 sheets defined 25.0% alpha, 15.4% beta 537 base pairs and 1039 stacking pairs defined. Time for finding SS restraints: 20.44 Creating SS restraints... 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 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 201 removed outlier: 4.073A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.219A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.753A pdb=" N SER D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.810A pdb=" N VAL D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.583A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.624A pdb=" N ARG E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 43 " --> pdb=" O MET E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.758A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.944A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 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 184 through 189 Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.807A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 4.318A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.394A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'K' and resid 111 through 118 removed outlier: 4.032A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 139 Processing helix chain 'N' and resid 9 through 23 removed outlier: 4.600A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 41 removed outlier: 3.784A pdb=" N GLU N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 54 removed outlier: 3.811A pdb=" N THR N 49 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 4.386A pdb=" N TYR N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 11 removed outlier: 4.105A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 104 removed outlier: 3.607A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 19 removed outlier: 4.335A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 44 through 49 Processing helix chain 'Q' and resid 51 through 56 Processing helix chain 'Q' and resid 57 through 70 removed outlier: 3.743A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 75 through 83 removed outlier: 3.651A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 112 removed outlier: 3.907A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 34 removed outlier: 3.720A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 removed outlier: 3.706A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 removed outlier: 3.966A pdb=" N ASP T 6 " --> pdb=" O ASP T 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 6' Processing helix chain 'T' and resid 14 through 21 removed outlier: 3.515A pdb=" N MET T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 48 removed outlier: 3.979A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 15 removed outlier: 3.628A pdb=" N ARG b 14 " --> pdb=" O LYS b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 18 No H-bonds generated for 'chain 'b' and resid 16 through 18' Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.708A pdb=" N ILE Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 2 through 6' Processing helix chain 'Y' and resid 9 through 33 removed outlier: 3.835A pdb=" N GLU Y 13 " --> pdb=" O LEU Y 9 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL Y 18 " --> pdb=" O ILE Y 14 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.184A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 17 removed outlier: 4.006A pdb=" N LYS d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 27 through 38 removed outlier: 3.827A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.505A pdb=" N LYS C 4 " --> pdb=" O THR C 18 " (cutoff:3.500A) 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 101 through 105 removed outlier: 6.463A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.729A 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: 3.506A pdb=" N ALA C 190 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 171 through 175 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.828A pdb=" N ASP D 180 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 189 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.786A pdb=" N ILE D 49 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.036A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.934A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 123 through 126 removed outlier: 7.041A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'K' and resid 7 through 9 removed outlier: 7.095A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 110 through 111 Processing sheet with id=AB7, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.651A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.770A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 43 through 49 removed outlier: 7.368A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 61 through 68 removed outlier: 3.767A pdb=" N VAL P 64 " --> pdb=" O ARG P 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 12 through 14 Processing sheet with id=AC3, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.555A pdb=" N LYS R 64 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 71 through 75 Processing sheet with id=AC5, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.372A pdb=" N SER S 101 " --> pdb=" O THR S 9 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR S 104 " --> pdb=" O ALA S 74 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AC7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.696A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 63 through 66 removed outlier: 3.666A pdb=" N TYR T 69 " --> pdb=" O VAL T 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.518A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 27 through 28 removed outlier: 3.618A pdb=" N LYS b 37 " --> pdb=" O THR b 28 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1265 hydrogen bonds 2026 hydrogen bond angles 0 basepair planarities 537 basepair parallelities 1039 stacking parallelities Total time for adding SS restraints: 68.16 Time building geometry restraints manager: 29.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6534 1.32 - 1.44: 29834 1.44 - 1.57: 25538 1.57 - 1.69: 4324 1.69 - 1.81: 79 Bond restraints: 66309 Sorted by residual: bond pdb=" CA HIS S 102 " pdb=" CB HIS S 102 " ideal model delta sigma weight residual 1.531 1.452 0.078 1.52e-02 4.33e+03 2.65e+01 bond pdb=" CB TRP Q 61 " pdb=" CG TRP Q 61 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.10e+00 bond pdb=" C5 G A2717 " pdb=" C6 G A2717 " ideal model delta sigma weight residual 1.419 1.373 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C5 G A1712 " pdb=" C6 G A1712 " ideal model delta sigma weight residual 1.419 1.373 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CB ARG d 34 " pdb=" CG ARG d 34 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.96e+00 ... (remaining 66304 not shown) Histogram of bond angle deviations from ideal: 82.24 - 93.27: 5 93.27 - 104.30: 8942 104.30 - 115.33: 49034 115.33 - 126.36: 35510 126.36 - 137.38: 6821 Bond angle restraints: 100312 Sorted by residual: angle pdb=" N HIS S 102 " pdb=" CA HIS S 102 " pdb=" C HIS S 102 " ideal model delta sigma weight residual 109.07 82.24 26.83 1.61e+00 3.86e-01 2.78e+02 angle pdb=" N ALA b 45 " pdb=" CA ALA b 45 " pdb=" C ALA b 45 " ideal model delta sigma weight residual 112.45 129.75 -17.30 1.39e+00 5.18e-01 1.55e+02 angle pdb=" C ARG D 84 " pdb=" CA ARG D 84 " pdb=" CB ARG D 84 " ideal model delta sigma weight residual 110.24 88.11 22.13 1.88e+00 2.83e-01 1.39e+02 angle pdb=" N ALA S 74 " pdb=" CA ALA S 74 " pdb=" C ALA S 74 " ideal model delta sigma weight residual 107.23 88.32 18.91 1.67e+00 3.59e-01 1.28e+02 angle pdb=" N ARG P 54 " pdb=" CA ARG P 54 " pdb=" C ARG P 54 " ideal model delta sigma weight residual 110.23 94.04 16.19 1.45e+00 4.76e-01 1.25e+02 ... (remaining 100307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 32289 35.98 - 71.97: 2244 71.97 - 107.95: 197 107.95 - 143.93: 25 143.93 - 179.91: 33 Dihedral angle restraints: 34788 sinusoidal: 29703 harmonic: 5085 Sorted by residual: dihedral pdb=" C ARG D 84 " pdb=" N ARG D 84 " pdb=" CA ARG D 84 " pdb=" CB ARG D 84 " ideal model delta harmonic sigma weight residual -122.60 -94.10 -28.50 0 2.50e+00 1.60e-01 1.30e+02 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 200.00 36.53 163.47 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U A 478 " pdb=" C1' U A 478 " pdb=" N1 U A 478 " pdb=" C2 U A 478 " ideal model delta sinusoidal sigma weight residual 200.00 38.05 161.95 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 34785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 12374 0.111 - 0.221: 584 0.221 - 0.332: 32 0.332 - 0.443: 17 0.443 - 0.553: 1 Chirality restraints: 13008 Sorted by residual: chirality pdb=" CA ARG D 84 " pdb=" N ARG D 84 " pdb=" C ARG D 84 " pdb=" CB ARG D 84 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C1' G A1246 " pdb=" O4' G A1246 " pdb=" C2' G A1246 " pdb=" N9 G A1246 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' G A 377 " pdb=" C4' G A 377 " pdb=" O3' G A 377 " pdb=" C2' G A 377 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 13005 not shown) Planarity restraints: 4580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 179 " -0.040 2.00e-02 2.50e+03 1.94e-02 1.04e+01 pdb=" N9 A A 179 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A A 179 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 179 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A A 179 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 179 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 179 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A A 179 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A A 179 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A 179 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1359 " -0.041 2.00e-02 2.50e+03 1.85e-02 1.03e+01 pdb=" N9 G A1359 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G A1359 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1359 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A1359 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A1359 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A1359 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A1359 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1359 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A1359 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A1359 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1359 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1712 " 0.042 2.00e-02 2.50e+03 1.82e-02 9.99e+00 pdb=" N9 G A1712 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G A1712 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1712 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1712 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1712 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A1712 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A1712 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A1712 " -0.004 2.00e-02 2.50e+03 ... (remaining 4577 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 25 2.08 - 2.78: 14689 2.78 - 3.49: 80159 3.49 - 4.19: 185383 4.19 - 4.90: 253285 Nonbonded interactions: 533541 Sorted by model distance: nonbonded pdb=" C2 U A 522 " pdb=" N6 A A 526 " model vdw 1.370 3.340 nonbonded pdb=" N2 G A1526 " pdb=" N2 G A1558 " model vdw 1.418 3.200 nonbonded pdb=" N3 U A 522 " pdb=" N6 A A 526 " model vdw 1.466 3.200 nonbonded pdb=" O2 U A 522 " pdb=" N6 A A 526 " model vdw 1.475 2.520 nonbonded pdb=" N2 G A 631 " pdb=" NZ LYS L 33 " model vdw 1.565 3.200 ... (remaining 533536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2169 5.49 5 S 43 5.16 5 C 29531 2.51 5 N 11276 2.21 5 O 17535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.450 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: 0.040 Extract box with map and model: 11.560 Check model and map are aligned: 0.710 Process input model: 184.270 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.420 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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 : 0.010 0.108 66309 Z= 0.595 Angle : 1.026 26.826 100312 Z= 0.528 Chirality : 0.054 0.553 13008 Planarity : 0.005 0.079 4580 Dihedral : 19.357 179.914 31508 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.31 % Favored : 88.66 % Rotamer Outliers : 6.50 % Cbeta Deviations : 0.30 % 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: -4.94 (0.15), residues: 1737 helix: -4.42 (0.12), residues: 431 sheet: -2.81 (0.25), residues: 317 loop : -2.95 (0.16), residues: 989 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 455 time to evaluate : 2.438 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 outliers start: 97 outliers final: 20 residues processed: 509 average time/residue: 0.6727 time to fit residues: 545.0055 Evaluate side-chains 317 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 2.456 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.4630 time to fit residues: 19.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.9980 chunk 294 optimal weight: 0.4980 chunk 163 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 226 optimal weight: 0.0040 chunk 352 optimal weight: 2.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 173 ASN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 179 ASN J 41 HIS J 78 HIS K 110 ASN L 4 HIS L 78 ASN N 68 ASN Q 37 GLN Q 66 ASN Q 81 HIS R 83 HIS S 73 GLN S 102 HIS T 35 ASN U 2 HIS U 64 HIS U 67 ASN b 40 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 66309 Z= 0.178 Angle : 0.688 8.205 100312 Z= 0.344 Chirality : 0.038 0.319 13008 Planarity : 0.005 0.101 4580 Dihedral : 18.427 179.891 27939 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.26 % Rotamer Outliers : 3.75 % 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: -3.94 (0.17), residues: 1737 helix: -3.08 (0.18), residues: 416 sheet: -2.41 (0.25), residues: 345 loop : -2.50 (0.17), residues: 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 358 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 392 average time/residue: 0.6207 time to fit residues: 402.2167 Evaluate side-chains 329 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 295 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4289 time to fit residues: 30.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 293 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 381 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 350 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS J 78 HIS K 3 GLN N 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 66309 Z= 0.242 Angle : 0.671 9.355 100312 Z= 0.337 Chirality : 0.037 0.296 13008 Planarity : 0.005 0.100 4580 Dihedral : 18.331 179.465 27939 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.75 % Favored : 90.96 % Rotamer Outliers : 3.49 % 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: -3.31 (0.18), residues: 1737 helix: -2.27 (0.22), residues: 431 sheet: -2.10 (0.26), residues: 344 loop : -2.20 (0.18), residues: 962 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 326 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 33 residues processed: 354 average time/residue: 0.6667 time to fit residues: 393.9415 Evaluate side-chains 320 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 287 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5000 time to fit residues: 33.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 237 optimal weight: 0.0970 chunk 354 optimal weight: 6.9990 chunk 375 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 29 ASN J 48 HIS ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN R 81 ASN R 101 ASN S 67 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 66309 Z= 0.289 Angle : 0.705 9.489 100312 Z= 0.354 Chirality : 0.039 0.382 13008 Planarity : 0.005 0.045 4580 Dihedral : 18.333 179.383 27939 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.06 % Favored : 91.77 % Rotamer Outliers : 4.02 % 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: -3.11 (0.18), residues: 1737 helix: -1.93 (0.23), residues: 436 sheet: -2.08 (0.25), residues: 346 loop : -2.12 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 308 time to evaluate : 2.547 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 34 residues processed: 344 average time/residue: 0.6187 time to fit residues: 352.5994 Evaluate side-chains 328 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 294 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4214 time to fit residues: 30.0721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 HIS ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN Q 108 GLN S 67 ASN U 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.095 66309 Z= 0.411 Angle : 0.827 10.032 100312 Z= 0.411 Chirality : 0.044 0.367 13008 Planarity : 0.006 0.058 4580 Dihedral : 18.644 179.314 27939 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.59 % Favored : 89.35 % Rotamer Outliers : 4.36 % 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: -3.19 (0.18), residues: 1737 helix: -1.96 (0.23), residues: 437 sheet: -2.11 (0.26), residues: 334 loop : -2.20 (0.18), residues: 966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 305 time to evaluate : 2.501 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 38 residues processed: 351 average time/residue: 0.6386 time to fit residues: 368.2462 Evaluate side-chains 318 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 280 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4408 time to fit residues: 34.4442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 8.9990 chunk 337 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN E 82 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN L 35 HIS L 126 ASN Q 108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 66309 Z= 0.257 Angle : 0.675 12.181 100312 Z= 0.338 Chirality : 0.038 0.314 13008 Planarity : 0.005 0.041 4580 Dihedral : 18.270 179.485 27939 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.23 % Favored : 91.71 % Rotamer Outliers : 2.88 % 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: -3.01 (0.18), residues: 1737 helix: -1.70 (0.24), residues: 443 sheet: -2.03 (0.26), residues: 343 loop : -2.14 (0.18), residues: 951 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 283 time to evaluate : 2.477 Fit side-chains outliers start: 43 outliers final: 23 residues processed: 310 average time/residue: 0.6696 time to fit residues: 342.1621 Evaluate side-chains 292 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 269 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4662 time to fit residues: 23.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 227 optimal weight: 0.0870 chunk 172 optimal weight: 10.0000 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 78 HIS ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 66309 Z= 0.263 Angle : 0.679 14.889 100312 Z= 0.340 Chirality : 0.038 0.304 13008 Planarity : 0.005 0.042 4580 Dihedral : 18.206 178.964 27939 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.33 % Favored : 90.62 % Rotamer Outliers : 1.81 % 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: -2.91 (0.19), residues: 1737 helix: -1.62 (0.24), residues: 444 sheet: -1.95 (0.26), residues: 353 loop : -2.07 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 276 time to evaluate : 2.457 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 286 average time/residue: 0.6390 time to fit residues: 300.6068 Evaluate side-chains 288 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4546 time to fit residues: 17.5655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 237 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS Q 108 GLN R 65 GLN S 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.106 66309 Z= 0.463 Angle : 0.870 15.651 100312 Z= 0.430 Chirality : 0.046 0.370 13008 Planarity : 0.006 0.062 4580 Dihedral : 18.697 179.498 27939 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.46 % Favored : 88.49 % Rotamer Outliers : 3.22 % 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: -3.23 (0.18), residues: 1737 helix: -1.90 (0.22), residues: 451 sheet: -2.00 (0.26), residues: 349 loop : -2.34 (0.18), residues: 937 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 280 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 311 average time/residue: 0.6337 time to fit residues: 325.2351 Evaluate side-chains 307 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4487 time to fit residues: 32.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 6.9990 chunk 358 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 314 optimal weight: 0.7980 chunk 329 optimal weight: 0.8980 chunk 347 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 49 HIS E 82 GLN K 4 GLN Q 108 GLN R 65 GLN R 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 66309 Z= 0.148 Angle : 0.602 14.686 100312 Z= 0.299 Chirality : 0.033 0.279 13008 Planarity : 0.004 0.046 4580 Dihedral : 17.950 179.302 27939 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.91 % Favored : 93.03 % Rotamer Outliers : 0.67 % 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: -2.81 (0.19), residues: 1737 helix: -1.47 (0.24), residues: 445 sheet: -1.85 (0.26), residues: 344 loop : -2.06 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 298 time to evaluate : 2.510 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 304 average time/residue: 0.6574 time to fit residues: 330.3167 Evaluate side-chains 290 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 288 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4376 time to fit residues: 4.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 1.9990 chunk 368 optimal weight: 0.0570 chunk 224 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 chunk 355 optimal weight: 0.2980 chunk 307 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 4 GLN S 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 66309 Z= 0.141 Angle : 0.560 17.078 100312 Z= 0.280 Chirality : 0.031 0.239 13008 Planarity : 0.004 0.057 4580 Dihedral : 17.629 178.147 27939 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer Outliers : 0.54 % 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: -2.51 (0.19), residues: 1737 helix: -1.23 (0.24), residues: 446 sheet: -1.50 (0.27), residues: 354 loop : -1.95 (0.19), residues: 937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 290 time to evaluate : 2.487 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 294 average time/residue: 0.6173 time to fit residues: 304.0532 Evaluate side-chains 282 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 279 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4443 time to fit residues: 4.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 283 optimal weight: 0.0770 chunk 45 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 316 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134459 restraints weight = 106899.835| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.07 r_work: 0.3507 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 66309 Z= 0.159 Angle : 0.567 16.570 100312 Z= 0.283 Chirality : 0.032 0.227 13008 Planarity : 0.004 0.054 4580 Dihedral : 17.551 178.621 27939 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.75 % Rotamer Outliers : 0.80 % 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: -2.40 (0.19), residues: 1737 helix: -1.11 (0.25), residues: 444 sheet: -1.40 (0.27), residues: 368 loop : -1.90 (0.19), residues: 925 =============================================================================== Job complete usr+sys time: 8653.37 seconds wall clock time: 156 minutes 0.93 seconds (9360.93 seconds total)