Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:19:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/02_2023/6ezo_4162_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/02_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_4162/02_2023/6ezo_4162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/02_2023/6ezo_4162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/02_2023/6ezo_4162_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezo_4162/02_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 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-dev-4877/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: 11.47, per 1000 atoms: 0.61 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: 6.76 Conformation dependent library (CDL) restraints added in 3.6 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: 2.07 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: 4.14 Time building geometry restraints manager: 7.29 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 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. 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: 0.780 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: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.250 Process input model: 45.880 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 2.124 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 182 average time/residue: 0.2456 time to fit residues: 73.9433 Evaluate side-chains 138 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1798 time to fit residues: 6.7209 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1532 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= 0.176 Angle : 0.654 17.554 26448 Z= 0.356 Chirality : 0.047 0.157 3353 Planarity : 0.005 0.055 3679 Dihedral : 7.121 162.303 3424 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.16 % Favored : 87.69 % 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: -4.48 (0.13), residues: 3315 helix: -1.96 (0.15), residues: 960 sheet: -3.16 (0.23), residues: 394 loop : -3.66 (0.12), residues: 1961 *********************** 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 146 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.178 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2387 time to fit residues: 59.9489 Evaluate side-chains 130 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7130 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 0.0370 chunk 326 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19043 Z= 0.301 Angle : 0.709 17.519 26448 Z= 0.386 Chirality : 0.049 0.164 3353 Planarity : 0.005 0.059 3679 Dihedral : 6.980 157.090 3424 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 18.58 % Favored : 81.27 % 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: -4.06 (0.14), residues: 3315 helix: -1.22 (0.16), residues: 963 sheet: -3.11 (0.23), residues: 410 loop : -3.58 (0.13), residues: 1942 *********************** 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 145 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2095 time to fit residues: 54.6692 Evaluate side-chains 126 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6208 ------------------------------------------------------------------------------- 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: 7.9990 chunk 156 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 144 optimal weight: 40.0000 chunk 202 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 320 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 19043 Z= 0.319 Angle : 0.710 18.003 26448 Z= 0.384 Chirality : 0.049 0.164 3353 Planarity : 0.005 0.055 3679 Dihedral : 6.955 150.675 3424 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.83 % Favored : 83.11 % 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: -3.89 (0.14), residues: 3315 helix: -0.96 (0.17), residues: 950 sheet: -3.02 (0.24), residues: 391 loop : -3.53 (0.13), residues: 1974 *********************** 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 : 2.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2122 time to fit residues: 55.0202 Evaluate side-chains 126 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8858 ------------------------------------------------------------------------------- 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: 20.0000 chunk 182 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 273 optimal weight: 7.9990 chunk 221 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 19043 Z= 0.312 Angle : 0.700 18.071 26448 Z= 0.377 Chirality : 0.049 0.177 3353 Planarity : 0.005 0.059 3679 Dihedral : 6.836 150.066 3424 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.79 % Favored : 80.09 % 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: -3.76 (0.14), residues: 3315 helix: -0.76 (0.18), residues: 942 sheet: -3.03 (0.24), residues: 420 loop : -3.46 (0.13), residues: 1953 *********************** 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 143 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2155 time to fit residues: 55.3562 Evaluate side-chains 128 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7689 ------------------------------------------------------------------------------- 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: 0.9990 chunk 288 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 148 optimal weight: 0.0980 chunk 26 optimal weight: 0.0060 chunk 106 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19043 Z= 0.149 Angle : 0.597 17.293 26448 Z= 0.310 Chirality : 0.046 0.172 3353 Planarity : 0.004 0.056 3679 Dihedral : 5.778 135.139 3424 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.98 % Favored : 88.96 % 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: -3.28 (0.15), residues: 3315 helix: -0.11 (0.18), residues: 942 sheet: -2.67 (0.25), residues: 388 loop : -3.32 (0.13), residues: 1985 *********************** 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 150 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2269 time to fit residues: 60.7254 Evaluate side-chains 127 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8090 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 234 optimal weight: 0.0000 chunk 181 optimal weight: 30.0000 chunk 270 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 319 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 30.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 19043 Z= 0.297 Angle : 0.677 17.204 26448 Z= 0.360 Chirality : 0.049 0.176 3353 Planarity : 0.005 0.060 3679 Dihedral : 6.218 128.223 3424 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 18.82 % Favored : 81.12 % 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: -3.41 (0.15), residues: 3315 helix: -0.27 (0.18), residues: 946 sheet: -2.84 (0.24), residues: 424 loop : -3.35 (0.14), residues: 1945 *********************** 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 140 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.439 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2262 time to fit residues: 56.9057 Evaluate side-chains 125 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8043 ------------------------------------------------------------------------------- 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: 7.9990 chunk 127 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19043 Z= 0.214 Angle : 0.624 17.132 26448 Z= 0.329 Chirality : 0.048 0.170 3353 Planarity : 0.004 0.056 3679 Dihedral : 5.899 123.089 3424 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.97 % Favored : 85.97 % 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: -3.21 (0.15), residues: 3315 helix: 0.01 (0.19), residues: 942 sheet: -2.73 (0.25), residues: 410 loop : -3.28 (0.13), residues: 1963 *********************** 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 143 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2175 time to fit residues: 56.1125 Evaluate side-chains 126 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5245 ------------------------------------------------------------------------------- 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: 8.9990 chunk 306 optimal weight: 8.9990 chunk 279 optimal weight: 0.0870 chunk 298 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 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: 3.9990 chunk 297 optimal weight: 0.0770 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 HIS H 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19043 Z= 0.378 Angle : 0.741 17.668 26448 Z= 0.399 Chirality : 0.050 0.194 3353 Planarity : 0.005 0.061 3679 Dihedral : 6.597 120.593 3424 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 20.81 % Favored : 79.10 % Rotamer Outliers : 0.18 % 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: -3.56 (0.15), residues: 3315 helix: -0.36 (0.18), residues: 935 sheet: -2.94 (0.25), residues: 419 loop : -3.45 (0.13), residues: 1961 *********************** 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: 1 poor density : 135 time to evaluate : 2.459 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2129 time to fit residues: 52.8050 Evaluate side-chains 126 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8534 ------------------------------------------------------------------------------- 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: 0.7980 chunk 315 optimal weight: 0.8980 chunk 192 optimal weight: 0.0020 chunk 149 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.002 0.033 19043 Z= 0.170 Angle : 0.610 17.290 26448 Z= 0.317 Chirality : 0.047 0.167 3353 Planarity : 0.004 0.054 3679 Dihedral : 5.749 121.225 3424 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.67 % Favored : 87.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.15), residues: 3315 helix: 0.19 (0.19), residues: 931 sheet: -2.70 (0.25), residues: 408 loop : -3.24 (0.14), residues: 1976 ********************** 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 142 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2082 time to fit residues: 53.6635 Evaluate side-chains 127 residues out of total 2937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7871 ------------------------------------------------------------------------------- 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: 5.9990 chunk 280 optimal weight: 0.0170 chunk 80 optimal weight: 0.0980 chunk 242 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 263 optimal weight: 0.0060 chunk 110 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107400 restraints weight = 42984.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106614 restraints weight = 65276.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106983 restraints weight = 67000.476| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 19043 Z= 0.140 Angle : 0.565 15.994 26448 Z= 0.288 Chirality : 0.046 0.180 3353 Planarity : 0.004 0.057 3679 Dihedral : 4.814 111.668 3424 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.71 (0.15), residues: 3315 helix: 0.59 (0.19), residues: 939 sheet: -2.48 (0.25), residues: 412 loop : -3.05 (0.14), residues: 1964 =============================================================================== Job complete usr+sys time: 2528.37 seconds wall clock time: 46 minutes 19.87 seconds (2779.87 seconds total)