Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 22:51:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/04_2023/6ezo_4162_updated.pdb" } resolution = 4.1 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 24 5.16 5 Cl 2 4.86 5 C 11676 2.51 5 N 3558 2.21 5 O 3498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18758 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1624 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 290 Chain: "B" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1627 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 299 Chain: "C" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1857 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 291} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 297 Chain: "D" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 1816 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 756 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 10, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 326 Chain: "E" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1812 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 881 Unresolved non-hydrogen angles: 1107 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 11, 'ASP:plan': 22, 'PHE:plan': 4, 'GLU:plan': 20, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 373 Chain: "F" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1806 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 3 Unresolved non-hydrogen bonds: 888 Unresolved non-hydrogen angles: 1116 Unresolved non-hydrogen dihedrals: 692 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 11, 'ASP:plan': 22, 'PHE:plan': 5, 'GLU:plan': 20, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 379 Chain: "G" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2013 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 18, 'TRANS': 336} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 764 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 13, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 355 Chain: "H" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1993 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 256} Link IDs: {'PTRANS': 18, 'TRANS': 334} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 769 Unresolved non-hydrogen angles: 976 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 13, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 358 Chain: "I" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2117 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1318 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 525 Chain: "J" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2063 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1062 Unresolved non-hydrogen angles: 1369 Unresolved non-hydrogen dihedrals: 838 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 7, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 19, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 552 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.94, per 1000 atoms: 0.58 Number of scatterers: 18758 At special positions: 0 Unit cell: (169.75, 131.25, 147, 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) Cl 2 17.00 S 24 16.00 O 3498 8.00 N 3558 7.00 C 11676 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: 7.52 Conformation dependent library (CDL) restraints added in 3.8 seconds 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 31 sheets defined 27.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.988A pdb=" N ARG A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 4.340A pdb=" N ALA A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 107 through 118 removed outlier: 5.645A pdb=" N THR A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.858A pdb=" N ALA A 167 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.999A pdb=" N GLU A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 4.391A pdb=" N CYS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.987A pdb=" N ARG B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 79 removed outlier: 4.340A pdb=" N ALA B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 107 through 118 removed outlier: 5.643A pdb=" N THR B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.858A pdb=" N ALA B 167 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 168 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 removed outlier: 4.001A pdb=" N GLU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 4.392A pdb=" N CYS B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 303 Processing helix chain 'C' and resid 13 through 24 removed outlier: 4.223A pdb=" N LEU C 22 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 24 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 47 Processing helix chain 'C' and resid 56 through 69 Processing helix chain 'C' and resid 76 through 95 Processing helix chain 'C' and resid 129 through 153 removed outlier: 4.167A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 152 " --> pdb=" O MET C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 4.147A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.213A pdb=" N LEU D 22 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D 24 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 47 Processing helix chain 'D' and resid 56 through 69 Processing helix chain 'D' and resid 76 through 95 Processing helix chain 'D' and resid 129 through 153 removed outlier: 4.166A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 removed outlier: 4.145A pdb=" N ALA D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 255 through 261 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 35 through 40 Proline residue: E 39 - end of helix No H-bonds generated for 'chain 'E' and resid 35 through 40' Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 114 through 122 removed outlier: 4.623A pdb=" N PHE E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 35 through 40 Proline residue: F 39 - end of helix No H-bonds generated for 'chain 'F' and resid 35 through 40' Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 114 through 122 removed outlier: 4.620A pdb=" N PHE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 213 through 216 No H-bonds generated for 'chain 'F' and resid 213 through 216' Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'G' and resid 207 through 215 removed outlier: 4.109A pdb=" N SER G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 239 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 257 through 266 Processing helix chain 'G' and resid 274 through 285 Processing helix chain 'G' and resid 293 through 310 removed outlier: 3.909A pdb=" N VAL G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 321 No H-bonds generated for 'chain 'G' and resid 318 through 321' Processing helix chain 'G' and resid 323 through 326 Processing helix chain 'G' and resid 370 through 373 No H-bonds generated for 'chain 'G' and resid 370 through 373' Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 424 through 426 No H-bonds generated for 'chain 'G' and resid 424 through 426' Processing helix chain 'G' and resid 474 through 476 No H-bonds generated for 'chain 'G' and resid 474 through 476' Processing helix chain 'G' and resid 509 through 517 Proline residue: G 513 - end of helix removed outlier: 4.068A pdb=" N ARG G 517 " --> pdb=" O VAL G 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 207 through 215 removed outlier: 4.110A pdb=" N SER H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 239 Processing helix chain 'H' and resid 250 through 255 Processing helix chain 'H' and resid 257 through 264 Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 293 through 310 removed outlier: 3.908A pdb=" N VAL H 308 " --> pdb=" O ILE H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 321 No H-bonds generated for 'chain 'H' and resid 318 through 321' Processing helix chain 'H' and resid 323 through 326 Processing helix chain 'H' and resid 370 through 373 No H-bonds generated for 'chain 'H' and resid 370 through 373' Processing helix chain 'H' and resid 388 through 390 No H-bonds generated for 'chain 'H' and resid 388 through 390' Processing helix chain 'H' and resid 424 through 426 No H-bonds generated for 'chain 'H' and resid 424 through 426' Processing helix chain 'H' and resid 474 through 476 No H-bonds generated for 'chain 'H' and resid 474 through 476' Processing helix chain 'H' and resid 509 through 517 Proline residue: H 513 - end of helix removed outlier: 4.064A pdb=" N ARG H 517 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 62 No H-bonds generated for 'chain 'I' and resid 59 through 62' Processing helix chain 'I' and resid 75 through 86 removed outlier: 3.879A pdb=" N THR I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU I 80 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 108 removed outlier: 4.196A pdb=" N LEU I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.538A pdb=" N ASP I 137 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP I 139 " --> pdb=" O ARG I 136 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA I 140 " --> pdb=" O ASP I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 170 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 218 through 220 No H-bonds generated for 'chain 'I' and resid 218 through 220' Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 254 through 261 removed outlier: 3.865A pdb=" N LEU I 259 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 275 Processing helix chain 'I' and resid 303 through 309 removed outlier: 3.868A pdb=" N ALA I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 75 through 86 removed outlier: 3.880A pdb=" N THR J 79 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU J 80 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 removed outlier: 4.197A pdb=" N LEU J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 141 removed outlier: 3.536A pdb=" N ASP J 137 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP J 139 " --> pdb=" O ARG J 136 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA J 140 " --> pdb=" O ASP J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 167 No H-bonds generated for 'chain 'J' and resid 164 through 167' Processing helix chain 'J' and resid 170 through 174 Processing helix chain 'J' and resid 218 through 220 No H-bonds generated for 'chain 'J' and resid 218 through 220' Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 254 through 261 removed outlier: 3.866A pdb=" N LEU J 259 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 275 Processing helix chain 'J' and resid 303 through 309 removed outlier: 3.867A pdb=" N ALA J 308 " --> pdb=" O HIS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing sheet with id= A, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.546A pdb=" N VAL A 152 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.543A pdb=" N VAL A 195 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.802A pdb=" N GLY A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 206 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 284 through 286 Processing sheet with id= E, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.546A pdb=" N VAL B 152 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.541A pdb=" N VAL B 195 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.804A pdb=" N GLY B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 206 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 208 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= I, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.674A pdb=" N ILE C 165 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 191 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 215 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLU C 193 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET C 217 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 245 through 248 removed outlier: 3.712A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 165 through 168 removed outlier: 3.662A pdb=" N ILE D 165 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU D 213 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL D 191 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU D 193 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET D 217 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 245 through 248 removed outlier: 3.713A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.558A pdb=" N ILE E 52 " --> pdb=" O VAL E 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 101 through 103 removed outlier: 3.639A pdb=" N VAL E 101 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 170 through 172 Processing sheet with id= P, first strand: chain 'E' and resid 396 through 398 removed outlier: 7.294A pdb=" N ALA E 413 " --> pdb=" O THR E 397 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 6 through 8 removed outlier: 6.559A pdb=" N ILE F 52 " --> pdb=" O VAL F 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 101 through 103 removed outlier: 3.639A pdb=" N VAL F 101 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 170 through 172 Processing sheet with id= T, first strand: chain 'F' and resid 379 through 381 removed outlier: 7.367A pdb=" N VAL F 396 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA F 413 " --> pdb=" O THR F 397 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'G' and resid 360 through 362 Processing sheet with id= V, first strand: chain 'G' and resid 407 through 409 removed outlier: 3.657A pdb=" N ALA G 407 " --> pdb=" O MET G 415 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 500 through 502 removed outlier: 3.870A pdb=" N GLY G 505 " --> pdb=" O THR G 502 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 360 through 362 Processing sheet with id= Y, first strand: chain 'H' and resid 407 through 409 removed outlier: 3.662A pdb=" N ALA H 407 " --> pdb=" O MET H 415 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.871A pdb=" N GLY H 505 " --> pdb=" O THR H 502 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 92 through 95 removed outlier: 6.919A pdb=" N ARG I 121 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS I 95 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE I 123 " --> pdb=" O CYS I 95 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'I' and resid 181 through 186 removed outlier: 4.645A pdb=" N ILE I 249 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS I 186 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS I 247 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 92 through 95 removed outlier: 6.921A pdb=" N ARG J 121 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N CYS J 95 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE J 123 " --> pdb=" O CYS J 95 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'J' and resid 204 through 206 Processing sheet with id= AE, first strand: chain 'J' and resid 181 through 186 removed outlier: 4.642A pdb=" N ILE J 249 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS J 186 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS J 247 " --> pdb=" O LYS J 186 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1404 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: 5.27 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3688 1.32 - 1.45: 4497 1.45 - 1.57: 10818 1.57 - 1.69: 0 1.69 - 1.82: 40 Bond restraints: 19043 Sorted by residual: bond pdb=" N ARG H 267 " pdb=" CA ARG H 267 " ideal model delta sigma weight residual 1.455 1.504 -0.049 9.60e-03 1.09e+04 2.64e+01 bond pdb=" C ALA D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.332 1.392 -0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" N PRO D 196 " pdb=" CD PRO D 196 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" CA ARG H 267 " pdb=" C ARG H 267 " ideal model delta sigma weight residual 1.519 1.565 -0.046 1.09e-02 8.42e+03 1.75e+01 bond pdb=" C20 C7B D 401 " pdb=" O06 C7B D 401 " ideal model delta sigma weight residual 1.347 1.428 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 19038 not shown) Histogram of bond angle deviations from ideal: 93.28 - 102.23: 46 102.23 - 111.19: 7406 111.19 - 120.14: 9425 120.14 - 129.10: 9458 129.10 - 138.05: 113 Bond angle restraints: 26448 Sorted by residual: angle pdb=" N GLY D 200 " pdb=" CA GLY D 200 " pdb=" C GLY D 200 " ideal model delta sigma weight residual 112.73 124.79 -12.06 1.20e+00 6.94e-01 1.01e+02 angle pdb=" N HIS C 201 " pdb=" CA HIS C 201 " pdb=" C HIS C 201 " ideal model delta sigma weight residual 111.07 121.80 -10.73 1.07e+00 8.73e-01 1.01e+02 angle pdb=" N SER A 22 " pdb=" CA SER A 22 " pdb=" C SER A 22 " ideal model delta sigma weight residual 111.28 101.17 10.11 1.09e+00 8.42e-01 8.61e+01 angle pdb=" C ARG G 267 " pdb=" N PRO G 268 " pdb=" CA PRO G 268 " ideal model delta sigma weight residual 119.93 110.31 9.62 1.07e+00 8.73e-01 8.09e+01 angle pdb=" N SER J 301 " pdb=" CA SER J 301 " pdb=" C SER J 301 " ideal model delta sigma weight residual 111.14 120.16 -9.02 1.08e+00 8.57e-01 6.98e+01 ... (remaining 26443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 10929 29.56 - 59.11: 68 59.11 - 88.67: 5 88.67 - 118.22: 0 118.22 - 147.78: 1 Dihedral angle restraints: 11003 sinusoidal: 1240 harmonic: 9763 Sorted by residual: dihedral pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual 122.80 139.47 -16.67 0 2.50e+00 1.60e-01 4.44e+01 dihedral pdb=" CA ALA G 421 " pdb=" C ALA G 421 " pdb=" N GLN G 422 " pdb=" CA GLN G 422 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ALA A 129 " pdb=" C ALA A 129 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 11000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2974 0.137 - 0.273: 341 0.273 - 0.410: 35 0.410 - 0.547: 2 0.547 - 0.683: 1 Chirality restraints: 3353 Sorted by residual: chirality pdb=" CA ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA ARG J 299 " pdb=" N ARG J 299 " pdb=" C ARG J 299 " pdb=" CB ARG J 299 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA THR C 253 " pdb=" N THR C 253 " pdb=" C THR C 253 " pdb=" CB THR C 253 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 3350 not shown) Planarity restraints: 3679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C09 C7B D 401 " 0.100 2.00e-02 2.50e+03 8.37e-02 8.75e+01 pdb=" C15 C7B D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C17 C7B D 401 " 0.074 2.00e-02 2.50e+03 pdb=" N07 C7B D 401 " -0.137 2.00e-02 2.50e+03 pdb=" O03 C7B D 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 C7B D 401 " -0.048 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" C16 C7B D 401 " -0.000 2.00e-02 2.50e+03 pdb=" C18 C7B D 401 " -0.032 2.00e-02 2.50e+03 pdb=" N08 C7B D 401 " 0.068 2.00e-02 2.50e+03 pdb=" O04 C7B D 401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 266 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C CYS H 266 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS H 266 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG H 267 " 0.021 2.00e-02 2.50e+03 ... (remaining 3676 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 8116 2.90 - 3.57: 24560 3.57 - 4.23: 33992 4.23 - 4.90: 54642 Nonbonded interactions: 121320 Sorted by model distance: nonbonded pdb=" O LEU G 473 " pdb=" CD1 TRP G 476 " model vdw 1.569 3.260 nonbonded pdb=" O ALA C 195 " pdb=" O PHE C 197 " model vdw 1.918 3.040 nonbonded pdb=" O HIS G 274 " pdb=" N ILE G 277 " model vdw 1.938 2.520 nonbonded pdb=" O HIS G 274 " pdb=" N ALA G 276 " model vdw 1.997 2.520 nonbonded pdb=" O LEU G 192 " pdb=" N PHE G 195 " model vdw 2.088 2.520 ... (remaining 121315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 129 or (resid 130 and (name N or name CA or name \ C or name O or name CB )) or resid 131 through 155 or (resid 156 and (name N or \ name CA or name C or name O or name CB )) or resid 157 through 271 or (resid 27 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 273 through \ 305)) selection = (chain 'B' and (resid 6 through 118 or (resid 119 through 121 and (name N or nam \ e CA or name C or name O or name CB )) or resid 122 through 148 or (resid 149 an \ d (name N or name CA or name C or name O or name CB )) or resid 150 through 158 \ or (resid 159 through 160 and (name N or name CA or name C or name O or name CB \ )) or resid 161 through 168 or (resid 169 through 172 and (name N or name CA or \ name C or name O or name CB )) or resid 173 through 177 or (resid 178 and (name \ N or name CA or name C or name O or name CB )) or resid 179 through 216 or (resi \ d 217 and (name N or name CA or name C or name O or name CB )) or resid 218 thro \ ugh 232 or (resid 233 through 234 and (name N or name CA or name C or name O or \ name CB )) or resid 235 through 305)) } ncs_group { reference = (chain 'C' and (resid 12 through 83 or (resid 84 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 153 or (resid 154 throu \ gh 157 and (name N or name CA or name C or name O or name CB )) or resid 158 thr \ ough 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) \ or resid 169 through 172 or (resid 173 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 178 or (resid 179 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 through 193 \ or (resid 194 through 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 202 or (resid 203 through 207 and (name N or name CA or \ name C or name O or name CB )) or resid 208 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 217 or (res \ id 218 through 221 and (name N or name CA or name C or name O or name CB )) or r \ esid 222 through 225 or (resid 226 through 227 and (name N or name CA or name C \ or name O or name CB )) or resid 228 through 229 or (resid 230 and (name N or na \ me CA or name C or name O or name CB )) or resid 231 through 237 or (resid 238 t \ hrough 239 and (name N or name CA or name C or name O or name CB )) or resid 240 \ through 245 or (resid 246 through 249 and (name N or name CA or name C or name \ O or name CB )) or resid 250 or (resid 251 and (name N or name CA or name C or n \ ame O or name CB )) or resid 252 or (resid 253 and (name N or name CA or name C \ or name O or name CB )) or resid 254 through 255 or (resid 256 through 259 and ( \ name N or name CA or name C or name O or name CB )) or resid 260 through 261 or \ (resid 262 through 263 and (name N or name CA or name C or name O or name CB )) \ or resid 264 through 266 or (resid 267 through 269 and (name N or name CA or nam \ e C or name O or name CB )) or resid 270 through 287 or (resid 288 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 through 349 \ )) selection = (chain 'D' and (resid 12 through 82 or (resid 83 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 96 or (resid 128 throug \ h 157 and (name N or name CA or name C or name O or name CB )) or resid 158 thro \ ugh 205 or (resid 206 through 207 and (name N or name CA or name C or name O or \ name CB )) or resid 208 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 293 or (resid 294 an \ d (name N or name CA or name C or name CB )) or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 307 or (resid 308 and ( \ name N or name CA or name C or name O or name CB )) or resid 309 or (resid 310 a \ nd (name N or name CA or name C or name O or name CB )) or resid 311 through 319 \ or (resid 320 through 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 or (resid 325 through 328 and (name N or name CA or name C or n \ ame O or name CB )) or resid 329 through 349)) } ncs_group { reference = (chain 'E' and (resid 1 through 66 or (resid 67 through 72 and (name N or name C \ A or name C or name O or name CB )) or resid 73 through 161 or (resid 162 throug \ h 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thro \ ugh 444)) selection = (chain 'F' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name CB )) or resid 162 through 444)) } ncs_group { reference = (chain 'G' and (resid 166 through 268 or (resid 269 through 273 and (name N or n \ ame CA or name C or name O or name CB )) or resid 274 through 343 or (resid 344 \ through 349 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 0 through 405 or (resid 406 through 411 and (name N or name CA or name C or name \ O or name CB )) or resid 412 through 481 or (resid 482 through 488 and (name N \ or name CA or name C or name O or name CB )) or resid 489 through 518)) selection = (chain 'H' and (resid 166 through 239 or (resid 240 through 242 and (name N or n \ ame CA or name C or name O or name CB )) or resid 243 through 518)) } ncs_group { reference = (chain 'I' and (resid 40 through 168 or (resid 169 through 189 and (name N or na \ me CA or name C or name O or name CB )) or resid 190 through 194 or (resid 195 t \ hrough 215 and (name N or name CA or name C or name O or name CB )) or resid 216 \ through 241 or (resid 242 through 259 and (name N or name CA or name C or name \ O or name CB )) or resid 260 through 288 or (resid 289 through 295 and (name N o \ r name CA or name C or name O or name CB )) or resid 296 through 311 or (resid 3 \ 12 through 316 and (name N or name CA or name C or name O or name CB )) or resid \ 317 through 342 or (resid 343 through 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 350 and (name N or name C \ A or name C or name O or name CB )) or resid 351 through 450)) selection = (chain 'J' and (resid 40 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 450)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 4.570 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 49.140 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.008 0.081 19043 Z= 0.552 Angle : 1.362 13.759 26448 Z= 0.894 Chirality : 0.092 0.683 3353 Planarity : 0.009 0.092 3679 Dihedral : 10.290 147.778 4637 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.75 % Allowed : 18.46 % Favored : 80.78 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.12), residues: 3315 helix: -3.47 (0.11), residues: 963 sheet: -3.58 (0.21), residues: 424 loop : -3.83 (0.12), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 2.332 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 0.2552 time to fit residues: 77.3439 Evaluate side-chains 138 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2076 time to fit residues: 7.9113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 100 optimal weight: 0.4980 chunk 158 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 HIS F 203 HIS G 182 HIS G 479 HIS H 182 HIS H 477 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19043 Z= 0.180 Angle : 0.641 10.773 26448 Z= 0.356 Chirality : 0.047 0.155 3353 Planarity : 0.005 0.054 3679 Dihedral : 7.010 162.345 3424 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.76 % Favored : 88.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.13), residues: 3315 helix: -1.90 (0.15), residues: 960 sheet: -3.14 (0.23), residues: 382 loop : -3.64 (0.12), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.130 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2328 time to fit residues: 59.9120 Evaluate side-chains 128 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 302 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS D 252 HIS G 477 GLN G 479 HIS H 479 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 19043 Z= 0.461 Angle : 0.826 11.306 26448 Z= 0.464 Chirality : 0.053 0.179 3353 Planarity : 0.007 0.066 3679 Dihedral : 7.787 153.536 3424 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 21.03 % Favored : 78.73 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.38 (0.13), residues: 3315 helix: -1.62 (0.16), residues: 961 sheet: -3.24 (0.23), residues: 398 loop : -3.70 (0.13), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2118 time to fit residues: 54.0632 Evaluate side-chains 120 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 144 optimal weight: 40.0000 chunk 202 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 182 HIS G 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19043 Z= 0.259 Angle : 0.667 10.790 26448 Z= 0.365 Chirality : 0.049 0.146 3353 Planarity : 0.005 0.054 3679 Dihedral : 6.915 149.309 3424 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.84 % Favored : 85.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.93 (0.14), residues: 3315 helix: -0.95 (0.17), residues: 945 sheet: -3.00 (0.24), residues: 399 loop : -3.58 (0.13), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2144 time to fit residues: 55.0490 Evaluate side-chains 126 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 10.0000 chunk 182 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 221 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 3.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 HIS G 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 19043 Z= 0.485 Angle : 0.833 12.921 26448 Z= 0.465 Chirality : 0.053 0.180 3353 Planarity : 0.007 0.076 3679 Dihedral : 7.721 145.713 3424 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 22.68 % Favored : 77.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.14), residues: 3315 helix: -1.30 (0.17), residues: 942 sheet: -3.22 (0.25), residues: 384 loop : -3.64 (0.13), residues: 1989 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.406 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2218 time to fit residues: 55.1137 Evaluate side-chains 124 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 0.4980 chunk 288 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 188 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 chunk 321 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 19043 Z= 0.165 Angle : 0.615 10.584 26448 Z= 0.332 Chirality : 0.047 0.155 3353 Planarity : 0.004 0.056 3679 Dihedral : 6.300 133.024 3424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.43 % Favored : 87.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.58 (0.14), residues: 3315 helix: -0.47 (0.18), residues: 941 sheet: -2.73 (0.26), residues: 377 loop : -3.48 (0.13), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2261 time to fit residues: 62.6243 Evaluate side-chains 133 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 30.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 19043 Z= 0.457 Angle : 0.798 12.533 26448 Z= 0.442 Chirality : 0.052 0.182 3353 Planarity : 0.006 0.074 3679 Dihedral : 7.220 125.916 3424 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 22.17 % Favored : 77.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.96 (0.14), residues: 3315 helix: -0.94 (0.17), residues: 940 sheet: -3.13 (0.25), residues: 403 loop : -3.59 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2203 time to fit residues: 54.5871 Evaluate side-chains 121 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 251 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 19043 Z= 0.170 Angle : 0.610 10.399 26448 Z= 0.328 Chirality : 0.047 0.172 3353 Planarity : 0.004 0.056 3679 Dihedral : 6.078 121.978 3424 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.40 % Favored : 87.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.43 (0.15), residues: 3315 helix: -0.21 (0.18), residues: 932 sheet: -2.63 (0.26), residues: 375 loop : -3.44 (0.13), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2266 time to fit residues: 59.7642 Evaluate side-chains 130 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 179 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 282 optimal weight: 0.4980 chunk 297 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 19043 Z= 0.472 Angle : 0.815 13.266 26448 Z= 0.451 Chirality : 0.053 0.193 3353 Planarity : 0.006 0.076 3679 Dihedral : 7.224 120.467 3424 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 22.32 % Favored : 77.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3315 helix: -0.82 (0.18), residues: 932 sheet: -3.09 (0.25), residues: 401 loop : -3.63 (0.13), residues: 1982 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2583 time to fit residues: 64.7631 Evaluate side-chains 121 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 0.8980 chunk 315 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 330 optimal weight: 0.0010 chunk 304 optimal weight: 10.0000 chunk 263 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 203 optimal weight: 0.4980 chunk 161 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 19043 Z= 0.178 Angle : 0.617 10.345 26448 Z= 0.331 Chirality : 0.047 0.176 3353 Planarity : 0.005 0.056 3679 Dihedral : 6.105 122.400 3424 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.67 % Favored : 87.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.15), residues: 3315 helix: -0.12 (0.19), residues: 926 sheet: -2.73 (0.25), residues: 401 loop : -3.42 (0.13), residues: 1988 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2257 time to fit residues: 60.8450 Evaluate side-chains 131 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099182 restraints weight = 45224.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098632 restraints weight = 98066.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099044 restraints weight = 98305.451| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 19043 Z= 0.522 Angle : 0.855 14.189 26448 Z= 0.474 Chirality : 0.054 0.195 3353 Planarity : 0.007 0.081 3679 Dihedral : 7.459 118.520 3424 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 23.20 % Favored : 76.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.02 (0.14), residues: 3315 helix: -0.93 (0.17), residues: 934 sheet: -3.05 (0.26), residues: 397 loop : -3.68 (0.13), residues: 1984 =============================================================================== Job complete usr+sys time: 2567.67 seconds wall clock time: 47 minutes 21.29 seconds (2841.29 seconds total)