Starting phenix.real_space_refine (version: dev) on Wed Apr 6 05:37:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/04_2022/7k0m_22602_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.121 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 18578 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'POV': 2, 'PLP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'POV': 2, 'PLP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 11.29, per 1000 atoms: 0.61 Number of scatterers: 18578 At special positions: 0 Unit cell: (151.755, 101.505, 118.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3352 8.00 N 3116 7.00 C 12006 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 2.9 seconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 47.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.155A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.587A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.022A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.769A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 454 through 472 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.891A pdb=" N TYR B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 125 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.726A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 437 through 456 Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.091A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 54 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'D' and resid 12 through 14 No H-bonds generated for 'chain 'D' and resid 12 through 14' Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 85 through 92 removed outlier: 6.142A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 121 through 137 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 31 through 54 Processing helix chain 'G' and resid 59 through 68 Processing helix chain 'H' and resid 12 through 14 No H-bonds generated for 'chain 'H' and resid 12 through 14' Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 45 through 65 Processing helix chain 'H' and resid 85 through 92 removed outlier: 6.142A pdb=" N ASP H 90 " --> pdb=" O TRP H 86 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 121 through 137 Proline residue: H 137 - end of helix Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'E' and resid 11 through 18 Processing helix chain 'E' and resid 22 through 39 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.155A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 214 through 230 removed outlier: 3.587A pdb=" N LYS E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 removed outlier: 4.023A pdb=" N VAL E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 322 through 331 removed outlier: 4.768A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 358 Processing helix chain 'E' and resid 361 through 377 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'F' and resid 68 through 93 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.917A pdb=" N TYR F 122 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN F 125 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 238 through 249 removed outlier: 3.725A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 359 through 362 No H-bonds generated for 'chain 'F' and resid 359 through 362' Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 392 through 400 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 437 through 456 Processing helix chain 'F' and resid 476 through 488 removed outlier: 4.090A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 535 Processing sheet with id= A, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.663A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= C, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.539A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.795A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.662A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP E 205 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 187 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS E 207 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 383 through 386 Processing sheet with id= G, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.539A pdb=" N LEU F 255 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU F 313 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 257 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLU F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ASP F 259 " --> pdb=" O GLU F 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR F 276 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER F 258 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG F 278 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.795A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2316 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: 5.31 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5932 1.34 - 1.46: 4212 1.46 - 1.58: 8648 1.58 - 1.70: 2 1.70 - 1.82: 170 Bond restraints: 18964 Sorted by residual: bond pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.79e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.741 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 18959 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.21: 220 103.21 - 110.90: 6819 110.90 - 118.60: 8123 118.60 - 126.29: 10214 126.29 - 133.99: 244 Bond angle restraints: 25620 Sorted by residual: angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 109.56 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 109.59 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.42 17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.43 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PLP F 603 " pdb=" P PLP F 603 " pdb=" O4P PLP F 603 " ideal model delta sigma weight residual 109.50 95.51 13.99 3.00e+00 1.11e-01 2.17e+01 ... (remaining 25615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 10825 23.30 - 46.61: 491 46.61 - 69.91: 34 69.91 - 93.21: 16 93.21 - 116.52: 2 Dihedral angle restraints: 11368 sinusoidal: 4582 harmonic: 6786 Sorted by residual: dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -167.06 -116.52 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" C5A PLP F 603 " pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " pdb=" O1P PLP F 603 " ideal model delta sinusoidal sigma weight residual 76.43 -167.07 -116.51 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" CA THR B 501 " pdb=" C THR B 501 " pdb=" N PRO B 502 " pdb=" CA PRO B 502 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2022 0.039 - 0.078: 596 0.078 - 0.117: 204 0.117 - 0.156: 28 0.156 - 0.195: 4 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA GLU E 400 " pdb=" N GLU E 400 " pdb=" C GLU E 400 " pdb=" CB GLU E 400 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 901 " -0.033 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C29 POV D 901 " 0.034 2.00e-02 2.50e+03 pdb="C210 POV D 901 " 0.032 2.00e-02 2.50e+03 pdb="C211 POV D 901 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV H 901 " 0.033 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C29 POV H 901 " -0.034 2.00e-02 2.50e+03 pdb="C210 POV H 901 " -0.032 2.00e-02 2.50e+03 pdb="C211 POV H 901 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 398 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C LEU E 398 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU E 398 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 399 " 0.014 2.00e-02 2.50e+03 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2680 2.75 - 3.29: 17275 3.29 - 3.83: 29791 3.83 - 4.36: 36073 4.36 - 4.90: 64342 Nonbonded interactions: 150161 Sorted by model distance: nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.219 2.440 nonbonded pdb=" NZ LYS E 264 " pdb=" O ASP E 299 " model vdw 2.226 2.520 nonbonded pdb=" NZ LYS A 264 " pdb=" O ASP A 299 " model vdw 2.226 2.520 nonbonded pdb=" OG1 THR D 84 " pdb=" OE1 GLU D 87 " model vdw 2.253 2.440 ... (remaining 150156 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 53 through 544) selection = (chain 'F' and resid 53 through 544) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 12006 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 10.750 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 50.480 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.005 0.213 18964 Z= 0.301 Angle : 0.686 18.105 25620 Z= 0.345 Chirality : 0.043 0.195 2854 Planarity : 0.004 0.053 3244 Dihedral : 12.846 116.518 7024 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2326 helix: 1.88 (0.16), residues: 1122 sheet: 0.35 (0.34), residues: 226 loop : -0.60 (0.20), residues: 978 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.174 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 1.5297 time to fit residues: 428.6888 Evaluate side-chains 175 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 429 GLN E 77 HIS E 372 GLN F 429 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18964 Z= 0.184 Angle : 0.488 6.461 25620 Z= 0.252 Chirality : 0.041 0.193 2854 Planarity : 0.004 0.051 3244 Dihedral : 6.883 89.378 2712 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2326 helix: 1.93 (0.15), residues: 1138 sheet: 0.28 (0.32), residues: 268 loop : -0.50 (0.21), residues: 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 2.371 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 189 average time/residue: 1.4567 time to fit residues: 307.2636 Evaluate side-chains 180 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.1743 time to fit residues: 8.0431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 187 optimal weight: 0.0870 chunk 209 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 372 GLN E 77 HIS E 372 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18964 Z= 0.184 Angle : 0.485 10.963 25620 Z= 0.248 Chirality : 0.041 0.182 2854 Planarity : 0.004 0.051 3244 Dihedral : 6.210 64.932 2712 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2326 helix: 1.82 (0.15), residues: 1166 sheet: 0.31 (0.32), residues: 266 loop : -0.49 (0.21), residues: 894 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 2.224 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 200 average time/residue: 1.4229 time to fit residues: 318.7255 Evaluate side-chains 183 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.6232 time to fit residues: 5.4620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 50.0000 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 372 GLN E 77 HIS E 372 GLN E 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 18964 Z= 0.241 Angle : 0.507 7.050 25620 Z= 0.262 Chirality : 0.042 0.184 2854 Planarity : 0.004 0.056 3244 Dihedral : 5.987 62.271 2712 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2326 helix: 1.77 (0.15), residues: 1152 sheet: 0.24 (0.32), residues: 266 loop : -0.52 (0.21), residues: 908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 2.166 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 200 average time/residue: 1.5787 time to fit residues: 352.6726 Evaluate side-chains 185 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.6691 time to fit residues: 7.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 0 optimal weight: 60.0000 chunk 114 optimal weight: 0.0970 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 372 GLN E 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 18964 Z= 0.312 Angle : 0.538 7.040 25620 Z= 0.279 Chirality : 0.044 0.184 2854 Planarity : 0.004 0.054 3244 Dihedral : 6.095 66.078 2712 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2326 helix: 1.69 (0.15), residues: 1140 sheet: -0.07 (0.33), residues: 250 loop : -0.60 (0.20), residues: 936 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 2.272 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 203 average time/residue: 1.4513 time to fit residues: 332.9379 Evaluate side-chains 180 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 1.0079 time to fit residues: 6.5521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 372 GLN B 441 GLN H 85 HIS E 372 GLN F 441 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18964 Z= 0.178 Angle : 0.467 6.486 25620 Z= 0.243 Chirality : 0.041 0.176 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.767 63.083 2712 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2326 helix: 1.79 (0.15), residues: 1164 sheet: 0.13 (0.32), residues: 270 loop : -0.56 (0.20), residues: 892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 2.743 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 205 average time/residue: 1.4327 time to fit residues: 329.6297 Evaluate side-chains 190 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.8796 time to fit residues: 10.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN E 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 18964 Z= 0.170 Angle : 0.464 8.602 25620 Z= 0.240 Chirality : 0.040 0.138 2854 Planarity : 0.004 0.055 3244 Dihedral : 5.599 62.261 2712 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2326 helix: 1.89 (0.15), residues: 1162 sheet: 0.07 (0.33), residues: 250 loop : -0.49 (0.20), residues: 914 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 2.117 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 197 average time/residue: 1.3568 time to fit residues: 301.3279 Evaluate side-chains 186 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.7334 time to fit residues: 9.2286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.0370 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.0670 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN E 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 18964 Z= 0.121 Angle : 0.432 7.553 25620 Z= 0.223 Chirality : 0.039 0.132 2854 Planarity : 0.004 0.046 3244 Dihedral : 5.280 59.995 2712 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2326 helix: 2.05 (0.16), residues: 1164 sheet: 0.34 (0.32), residues: 266 loop : -0.46 (0.21), residues: 896 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 2.395 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 205 average time/residue: 1.4051 time to fit residues: 324.9693 Evaluate side-chains 185 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.3600 time to fit residues: 4.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 0.4980 chunk 214 optimal weight: 0.0670 chunk 125 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 372 GLN E 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18964 Z= 0.206 Angle : 0.488 8.049 25620 Z= 0.251 Chirality : 0.041 0.138 2854 Planarity : 0.004 0.064 3244 Dihedral : 5.454 59.624 2712 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2326 helix: 1.94 (0.15), residues: 1164 sheet: 0.40 (0.32), residues: 268 loop : -0.50 (0.21), residues: 894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 2.057 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 195 average time/residue: 1.3751 time to fit residues: 303.3641 Evaluate side-chains 187 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.6053 time to fit residues: 5.2718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 0.0370 chunk 231 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 0.0970 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 18964 Z= 0.139 Angle : 0.453 8.295 25620 Z= 0.233 Chirality : 0.040 0.135 2854 Planarity : 0.004 0.058 3244 Dihedral : 5.282 58.839 2712 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2326 helix: 2.04 (0.16), residues: 1164 sheet: 0.41 (0.32), residues: 268 loop : -0.46 (0.21), residues: 894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 2.194 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 187 average time/residue: 1.3491 time to fit residues: 284.6277 Evaluate side-chains 183 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.2029 time to fit residues: 3.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 184 optimal weight: 0.3980 chunk 77 optimal weight: 0.0040 chunk 189 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.6712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN E 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102257 restraints weight = 22785.081| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.45 r_work: 0.3129 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work: 0.3100 rms_B_bonded: 2.23 restraints_weight: 0.1250 r_work: 0.3086 rms_B_bonded: 2.30 restraints_weight: 0.0625 r_work: 0.3071 rms_B_bonded: 2.41 restraints_weight: 0.0312 r_work: 0.3055 rms_B_bonded: 2.54 restraints_weight: 0.0156 r_work: 0.3038 rms_B_bonded: 2.71 restraints_weight: 0.0078 r_work: 0.3020 rms_B_bonded: 2.90 restraints_weight: 0.0039 r_work: 0.3002 rms_B_bonded: 3.13 restraints_weight: 0.0020 r_work: 0.2983 rms_B_bonded: 3.38 restraints_weight: 0.0010 r_work: 0.2962 rms_B_bonded: 3.67 restraints_weight: 0.0005 r_work: 0.2940 rms_B_bonded: 4.00 restraints_weight: 0.0002 r_work: 0.2917 rms_B_bonded: 4.37 restraints_weight: 0.0001 r_work: 0.2893 rms_B_bonded: 4.78 restraints_weight: 0.0001 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 18964 Z= 0.165 Angle : 0.465 8.166 25620 Z= 0.239 Chirality : 0.040 0.136 2854 Planarity : 0.004 0.067 3244 Dihedral : 5.290 58.321 2712 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2326 helix: 1.99 (0.15), residues: 1164 sheet: 0.42 (0.32), residues: 268 loop : -0.46 (0.21), residues: 894 =============================================================================== Job complete usr+sys time: 5550.24 seconds wall clock time: 100 minutes 20.53 seconds (6020.53 seconds total)