Starting phenix.real_space_refine (version: dev) on Fri Feb 24 05:30:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h25_0128/02_2023/6h25_0128.pdb" } resolution = 3.8 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= 0.008 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 "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "I ARG 6": "NH1" <-> "NH2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 129": "NH1" <-> "NH2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J ARG 407": "NH1" <-> "NH2" Residue "J ARG 624": "NH1" <-> "NH2" Residue "J GLU 712": "OE1" <-> "OE2" Residue "J ARG 741": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22138 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2221 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1771 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 231} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1923 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1570 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2144 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1752 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1527 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2066 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "I" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 373 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 6488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6488 Classifications: {'peptide': 868} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 43, 'TRANS': 824} Chain breaks: 3 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 295 Chain: "K" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 183 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 12.90, per 1000 atoms: 0.58 Number of scatterers: 22138 At special positions: 0 Unit cell: (137.7, 143.1, 152.55, 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 126 16.00 P 6 15.00 O 4158 8.00 N 3938 7.00 C 13910 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: 8.11 Conformation dependent library (CDL) restraints added in 3.3 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 40 sheets defined 31.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.636A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.627A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 243 through 277 removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 removed outlier: 4.500A pdb=" N SER B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.641A pdb=" N LEU B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.531A pdb=" N GLY B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 244 removed outlier: 3.853A pdb=" N ASP B 229 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.517A pdb=" N GLN C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.511A pdb=" N ASP C 123 " --> pdb=" O GLN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.694A pdb=" N ALA C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 244 through 273 removed outlier: 3.511A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.767A pdb=" N CYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 202 through 232 removed outlier: 3.533A pdb=" N ARG D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.768A pdb=" N LEU E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 147 through 162 removed outlier: 4.270A pdb=" N ALA E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 221 Processing helix chain 'E' and resid 248 through 280 removed outlier: 3.860A pdb=" N ILE E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.320A pdb=" N TYR F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 3.937A pdb=" N GLU F 121 " --> pdb=" O CYS F 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.808A pdb=" N ALA F 160 " --> pdb=" O SER F 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 233 through 266 Proline residue: F 253 - end of helix removed outlier: 3.653A pdb=" N ARG F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.559A pdb=" N ILE G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 225 removed outlier: 3.682A pdb=" N GLU G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 256 Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 175 through 179 removed outlier: 4.174A pdb=" N VAL H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 3.620A pdb=" N ASN H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 264 Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.715A pdb=" N ILE H 271 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU H 272 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 291 Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 102 through 115 removed outlier: 3.553A pdb=" N ASN J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 163 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 200 Processing helix chain 'J' and resid 203 through 207 removed outlier: 3.989A pdb=" N GLU J 206 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 298 through 302 removed outlier: 3.512A pdb=" N TRP J 302 " --> pdb=" O LYS J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 437 removed outlier: 3.768A pdb=" N HIS J 437 " --> pdb=" O LEU J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 451 removed outlier: 3.529A pdb=" N SER J 450 " --> pdb=" O GLN J 446 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE J 451 " --> pdb=" O ALA J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 464 removed outlier: 3.686A pdb=" N ASP J 463 " --> pdb=" O THR J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 541 through 547 Processing helix chain 'J' and resid 589 through 599 Processing helix chain 'J' and resid 604 through 628 removed outlier: 3.589A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE J 625 " --> pdb=" O LYS J 621 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 626 " --> pdb=" O LYS J 622 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY J 628 " --> pdb=" O ARG J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 657 through 683 removed outlier: 4.225A pdb=" N SER J 661 " --> pdb=" O ARG J 657 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER J 683 " --> pdb=" O HIS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 709 removed outlier: 3.702A pdb=" N ILE J 701 " --> pdb=" O SER J 697 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU J 702 " --> pdb=" O ASN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 727 Processing helix chain 'J' and resid 733 through 747 removed outlier: 3.954A pdb=" N ASN J 737 " --> pdb=" O PHE J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 781 through 795 removed outlier: 3.543A pdb=" N VAL J 785 " --> pdb=" O ARG J 781 " (cutoff:3.500A) Processing helix chain 'J' and resid 801 through 805 Processing helix chain 'J' and resid 806 through 842 removed outlier: 3.599A pdb=" N LEU J 810 " --> pdb=" O ASP J 806 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 822 " --> pdb=" O ASN J 818 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 823 " --> pdb=" O PHE J 819 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 825 " --> pdb=" O HIS J 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR J 826 " --> pdb=" O LYS J 822 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 885 Processing helix chain 'K' and resid 82 through 96 removed outlier: 3.758A pdb=" N LYS K 86 " --> pdb=" O PRO K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.391A pdb=" N ILE A 75 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 134 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 77 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 136 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 79 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 138 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU A 81 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.805A pdb=" N TRP A 130 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS A 122 " --> pdb=" O TRP A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.704A pdb=" N TYR A 204 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 220 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 236 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 222 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 234 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 224 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 233 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 203 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN A 235 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET B 201 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 237 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU B 199 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 195 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA B 188 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 199 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 201 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN B 184 " --> pdb=" O MET B 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 6.264A pdb=" N LYS B 47 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 71 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE B 123 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 73 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL B 125 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 75 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL B 127 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER B 77 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLN B 129 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP C 133 " --> pdb=" O CYS C 125 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS C 125 " --> pdb=" O TRP C 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 84 removed outlier: 7.130A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 174 through 178 removed outlier: 4.600A pdb=" N GLU C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.394A pdb=" N THR C 223 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C 235 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 225 " --> pdb=" O CYS C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.208A pdb=" N SER D 53 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 117 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 115 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.555A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.676A pdb=" N TRP E 133 " --> pdb=" O CYS E 125 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 125 " --> pdb=" O TRP E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 78 through 85 removed outlier: 7.542A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU E 143 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP E 57 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 35 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 210 through 212 removed outlier: 4.229A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 229 " --> pdb=" O CYS E 238 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N CYS E 238 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 239 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU F 225 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY E 243 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA F 223 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA F 214 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU F 225 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 212 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY F 227 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY F 210 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.628A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS F 61 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 145 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN F 143 " --> pdb=" O PRO F 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 144 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 146 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 27 through 28 removed outlier: 3.948A pdb=" N GLY G 84 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG G 85 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 103 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AC1, first strand: chain 'G' and resid 191 through 192 removed outlier: 7.000A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER G 140 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS G 124 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS G 130 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 165 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 199 through 201 removed outlier: 4.096A pdb=" N LEU G 227 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE K 77 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'H' and resid 164 through 165 removed outlier: 7.110A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 156 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU H 109 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL H 91 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS H 97 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AC7, first strand: chain 'I' and resid 7 through 8 removed outlier: 8.016A pdb=" N VAL I 55 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 13 through 15 removed outlier: 7.028A pdb=" N ILE I 33 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 66 through 68 removed outlier: 5.721A pdb=" N PHE J 173 " --> pdb=" O PHE J 192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 87 through 91 removed outlier: 7.036A pdb=" N VAL J 88 " --> pdb=" O TYR J 121 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE J 123 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL J 90 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 274 through 278 removed outlier: 7.540A pdb=" N ILE J 291 " --> pdb=" O ILE J 348 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 348 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA J 293 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 356 through 361 removed outlier: 3.805A pdb=" N LEU J 372 " --> pdb=" O SER J 361 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG J 384 " --> pdb=" O GLY J 414 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 416 " --> pdb=" O ARG J 384 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN J 413 " --> pdb=" O ASP J 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 417 " --> pdb=" O ILE J 399 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE J 399 " --> pdb=" O VAL J 417 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN J 419 " --> pdb=" O ARG J 397 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ARG J 397 " --> pdb=" O ASN J 419 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG J 396 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU J 360 " --> pdb=" O ARG J 396 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 468 through 469 removed outlier: 6.464A pdb=" N GLU J 468 " --> pdb=" O VAL J 581 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN J 583 " --> pdb=" O GLU J 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS J 574 " --> pdb=" O GLU J 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 476 through 478 removed outlier: 6.517A pdb=" N SER J 477 " --> pdb=" O LEU J 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AD8, first strand: chain 'J' and resid 638 through 640 Processing sheet with id=AD9, first strand: chain 'J' and resid 687 through 690 Processing sheet with id=AE1, first strand: chain 'J' and resid 847 through 848 removed outlier: 3.620A pdb=" N GLU J 848 " --> pdb=" O VAL J 909 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 909 " --> pdb=" O GLU J 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 851 through 855 removed outlier: 7.011A pdb=" N VAL J 861 " --> pdb=" O LEU J 853 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL J 855 " --> pdb=" O ALA J 859 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA J 859 " --> pdb=" O VAL J 855 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 886 through 887 removed outlier: 3.643A pdb=" N LEU J 894 " --> pdb=" O PHE J 901 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 912 through 914 removed outlier: 3.554A pdb=" N LYS J 922 " --> pdb=" O ASP J 914 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3750 1.31 - 1.44: 5445 1.44 - 1.57: 13124 1.57 - 1.69: 12 1.69 - 1.82: 172 Bond restraints: 22503 Sorted by residual: bond pdb=" C ILE B 25 " pdb=" O ILE B 25 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.07e-02 8.73e+03 2.36e+01 bond pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 22498 not shown) Histogram of bond angle deviations from ideal: 97.19 - 105.00: 480 105.00 - 112.80: 12334 112.80 - 120.61: 9934 120.61 - 128.42: 7676 128.42 - 136.22: 149 Bond angle restraints: 30573 Sorted by residual: angle pdb=" N GLU E 181 " pdb=" CA GLU E 181 " pdb=" C GLU E 181 " ideal model delta sigma weight residual 111.07 126.81 -15.74 1.07e+00 8.73e-01 2.16e+02 angle pdb=" CA PRO J 802 " pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 112.00 98.29 13.71 1.40e+00 5.10e-01 9.59e+01 angle pdb=" CA PRO J 883 " pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 112.00 98.31 13.69 1.40e+00 5.10e-01 9.56e+01 angle pdb=" CA PRO J 881 " pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 112.00 98.46 13.54 1.40e+00 5.10e-01 9.36e+01 angle pdb=" CA PRO J 770 " pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.14e+01 ... (remaining 30568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 13260 23.15 - 46.31: 392 46.31 - 69.46: 17 69.46 - 92.61: 9 92.61 - 115.77: 2 Dihedral angle restraints: 13680 sinusoidal: 5128 harmonic: 8552 Sorted by residual: dihedral pdb=" O4' U R 40 " pdb=" C1' U R 40 " pdb=" N1 U R 40 " pdb=" C2 U R 40 " ideal model delta sinusoidal sigma weight residual -160.00 -44.23 -115.77 1 1.50e+01 4.44e-03 6.12e+01 dihedral pdb=" CD ARG C 23 " pdb=" NE ARG C 23 " pdb=" CZ ARG C 23 " pdb=" NH1 ARG C 23 " ideal model delta sinusoidal sigma weight residual 0.00 65.72 -65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CA SER J 57 " pdb=" C SER J 57 " pdb=" N SER J 58 " pdb=" CA SER J 58 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 13677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3487 0.124 - 0.249: 127 0.249 - 0.373: 10 0.373 - 0.497: 2 0.497 - 0.622: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CA GLU E 181 " pdb=" N GLU E 181 " pdb=" C GLU E 181 " pdb=" CB GLU E 181 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CA ASN J 603 " pdb=" N ASN J 603 " pdb=" C ASN J 603 " pdb=" CB ASN J 603 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA LYS J 118 " pdb=" N LYS J 118 " pdb=" C LYS J 118 " pdb=" CB LYS J 118 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3624 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 23 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 23 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 23 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 23 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 880 " -0.128 5.00e-02 4.00e+02 1.80e-01 5.17e+01 pdb=" N PRO J 881 " 0.310 5.00e-02 4.00e+02 pdb=" CA PRO J 881 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO J 881 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 882 " 0.104 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO J 883 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO J 883 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO J 883 " 0.074 5.00e-02 4.00e+02 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 5 1.86 - 2.62: 246 2.62 - 3.38: 27378 3.38 - 4.14: 48735 4.14 - 4.90: 85953 Nonbonded interactions: 162317 Sorted by model distance: nonbonded pdb=" OG SER J 599 " pdb=" OD1 ASN J 601 " model vdw 1.101 2.440 nonbonded pdb=" CE2 PHE J 840 " pdb=" CG2 ILE J 911 " model vdw 1.407 3.760 nonbonded pdb=" O ARG K 78 " pdb=" N PHE K 80 " model vdw 1.583 2.520 nonbonded pdb=" NE2 GLN J 837 " pdb=" O GLN J 921 " model vdw 1.641 2.520 nonbonded pdb=" CD LYS A 267 " pdb=" OE2 GLU A 286 " model vdw 1.808 3.440 ... (remaining 162312 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 6 5.49 5 S 126 5.16 5 C 13910 2.51 5 N 3938 2.21 5 O 4158 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.960 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: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.310 Process input model: 56.420 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 22503 Z= 0.407 Angle : 1.096 15.735 30573 Z= 0.650 Chirality : 0.060 0.622 3627 Planarity : 0.011 0.448 3956 Dihedral : 10.985 115.768 8146 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.67 % Favored : 93.92 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.04 % 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 (0.13), residues: 2929 helix: -1.64 (0.14), residues: 842 sheet: -0.65 (0.20), residues: 639 loop : -2.55 (0.13), residues: 1448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 898 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 12 residues processed: 925 average time/residue: 0.3932 time to fit residues: 532.0011 Evaluate side-chains 572 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 560 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2780 time to fit residues: 8.9689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 141 HIS A 159 HIS A 189 HIS B 102 GLN C 38 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 192 HIS D 30 HIS D 214 GLN D 229 GLN E 115 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN F 257 GLN H 247 GLN J 92 GLN J 127 HIS J 146 ASN J 157 ASN J 170 GLN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 671 ASN J 737 ASN J 763 HIS ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 828 GLN J 835 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22503 Z= 0.288 Angle : 0.683 9.029 30573 Z= 0.355 Chirality : 0.045 0.282 3627 Planarity : 0.005 0.070 3956 Dihedral : 6.563 105.305 3254 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer Outliers : 5.74 % 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: -1.38 (0.15), residues: 2929 helix: 0.42 (0.17), residues: 849 sheet: -0.43 (0.20), residues: 663 loop : -2.02 (0.15), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 621 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 70 residues processed: 698 average time/residue: 0.3333 time to fit residues: 361.5918 Evaluate side-chains 587 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 517 time to evaluate : 2.551 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.1997 time to fit residues: 29.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 235 GLN B 102 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 164 GLN D 30 HIS D 49 GLN D 173 GLN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS J 763 HIS ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 837 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 22503 Z= 0.213 Angle : 0.622 10.438 30573 Z= 0.315 Chirality : 0.043 0.223 3627 Planarity : 0.004 0.055 3956 Dihedral : 6.157 100.982 3254 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.84 % Rotamer Outliers : 2.71 % 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: -0.81 (0.15), residues: 2929 helix: 1.16 (0.17), residues: 852 sheet: -0.36 (0.19), residues: 669 loop : -1.74 (0.15), residues: 1408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 565 time to evaluate : 2.481 Fit side-chains TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 603 average time/residue: 0.3393 time to fit residues: 318.1350 Evaluate side-chains 536 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 507 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2589 time to fit residues: 16.4467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 6.9990 chunk 199 optimal weight: 0.0030 chunk 137 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 178 optimal weight: 0.0870 chunk 266 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 252 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 overall best weight: 0.5908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 102 GLN C 162 ASN E 44 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 788 HIS ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 920 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22503 Z= 0.171 Angle : 0.593 8.952 30573 Z= 0.297 Chirality : 0.042 0.175 3627 Planarity : 0.004 0.054 3956 Dihedral : 5.833 97.916 3254 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer Outliers : 2.71 % 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: -0.46 (0.15), residues: 2929 helix: 1.57 (0.18), residues: 853 sheet: -0.11 (0.20), residues: 636 loop : -1.61 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 547 time to evaluate : 2.485 Fit side-chains TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 581 average time/residue: 0.3359 time to fit residues: 305.5617 Evaluate side-chains 539 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 508 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2155 time to fit residues: 16.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 0.9980 chunk 160 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 102 GLN B 105 GLN C 162 ASN E 44 ASN E 271 GLN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 569 ASN J 788 HIS ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22503 Z= 0.172 Angle : 0.575 11.548 30573 Z= 0.288 Chirality : 0.042 0.164 3627 Planarity : 0.003 0.052 3956 Dihedral : 5.633 94.502 3254 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer Outliers : 2.05 % 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: -0.26 (0.15), residues: 2929 helix: 1.81 (0.18), residues: 854 sheet: -0.05 (0.20), residues: 635 loop : -1.51 (0.16), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 550 time to evaluate : 2.541 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 574 average time/residue: 0.3261 time to fit residues: 293.9216 Evaluate side-chains 534 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 508 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2052 time to fit residues: 13.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 282 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 103 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS A 235 GLN C 162 ASN E 44 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 HIS ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 22503 Z= 0.251 Angle : 0.622 14.855 30573 Z= 0.312 Chirality : 0.043 0.197 3627 Planarity : 0.004 0.058 3956 Dihedral : 5.682 93.594 3254 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer Outliers : 2.80 % 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: -0.17 (0.15), residues: 2929 helix: 1.89 (0.18), residues: 855 sheet: 0.06 (0.21), residues: 597 loop : -1.46 (0.15), residues: 1477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 519 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 39 residues processed: 551 average time/residue: 0.3362 time to fit residues: 289.5977 Evaluate side-chains 532 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 493 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2127 time to fit residues: 18.9431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 160 optimal weight: 0.0970 chunk 206 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 129 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 103 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 ASN ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 22503 Z= 0.257 Angle : 0.623 12.939 30573 Z= 0.312 Chirality : 0.043 0.168 3627 Planarity : 0.004 0.057 3956 Dihedral : 5.704 92.823 3254 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer Outliers : 1.65 % 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: -0.15 (0.15), residues: 2929 helix: 1.90 (0.18), residues: 858 sheet: -0.03 (0.21), residues: 606 loop : -1.41 (0.16), residues: 1465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 538 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 556 average time/residue: 0.3496 time to fit residues: 304.9008 Evaluate side-chains 525 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 504 time to evaluate : 2.640 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2118 time to fit residues: 12.2740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 34 ASN A 235 GLN C 162 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 22503 Z= 0.265 Angle : 0.648 13.422 30573 Z= 0.323 Chirality : 0.044 0.176 3627 Planarity : 0.004 0.055 3956 Dihedral : 5.710 92.528 3254 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer Outliers : 1.87 % 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: -0.15 (0.15), residues: 2929 helix: 1.91 (0.18), residues: 858 sheet: 0.03 (0.21), residues: 588 loop : -1.42 (0.15), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 521 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 538 average time/residue: 0.3616 time to fit residues: 300.6504 Evaluate side-chains 529 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 502 time to evaluate : 2.779 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2098 time to fit residues: 14.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 0.0060 chunk 269 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 34 ASN A 235 GLN B 105 GLN H 199 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 22503 Z= 0.169 Angle : 0.619 15.474 30573 Z= 0.303 Chirality : 0.042 0.178 3627 Planarity : 0.004 0.049 3956 Dihedral : 5.488 88.543 3254 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer Outliers : 0.58 % 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: -0.03 (0.16), residues: 2929 helix: 2.07 (0.18), residues: 854 sheet: 0.06 (0.21), residues: 592 loop : -1.38 (0.15), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 545 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 551 average time/residue: 0.3592 time to fit residues: 303.8182 Evaluate side-chains 511 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 502 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2029 time to fit residues: 7.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 290 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 231 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 235 GLN B 116 HIS ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 22503 Z= 0.265 Angle : 0.667 14.747 30573 Z= 0.330 Chirality : 0.044 0.223 3627 Planarity : 0.004 0.053 3956 Dihedral : 5.587 87.708 3254 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.92 % Rotamer Outliers : 0.85 % 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: -0.11 (0.16), residues: 2929 helix: 2.00 (0.18), residues: 855 sheet: -0.03 (0.21), residues: 602 loop : -1.40 (0.15), residues: 1472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 507 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 513 average time/residue: 0.3572 time to fit residues: 283.9887 Evaluate side-chains 506 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 493 time to evaluate : 2.602 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2283 time to fit residues: 9.0344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.0000 chunk 246 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN A 235 GLN C 162 ASN ** J 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140833 restraints weight = 31421.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.143788 restraints weight = 18928.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144911 restraints weight = 12163.844| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 22503 Z= 0.161 Angle : 0.631 15.513 30573 Z= 0.309 Chirality : 0.042 0.202 3627 Planarity : 0.004 0.047 3956 Dihedral : 5.371 82.620 3254 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer Outliers : 0.27 % 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: 0.01 (0.16), residues: 2929 helix: 2.07 (0.18), residues: 858 sheet: 0.18 (0.21), residues: 576 loop : -1.36 (0.15), residues: 1495 =============================================================================== Job complete usr+sys time: 5619.40 seconds wall clock time: 101 minutes 18.91 seconds (6078.91 seconds total)