Starting phenix.real_space_refine (version: dev) on Wed Feb 22 22:33:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/02_2023/7k0m_22602_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/02_2023/7k0m_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_22602/02_2023/7k0m_22602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/02_2023/7k0m_22602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/02_2023/7k0m_22602_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0m_22602/02_2023/7k0m_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 Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E GLU 458": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 304": "NH1" <-> "NH2" Residue "F ARG 305": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 452": "NH1" <-> "NH2" Residue "F ARG 484": "NH1" <-> "NH2" Residue "F ARG 507": "NH1" <-> "NH2" 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-4877/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: {'PLP': 1, 'POV': 2} 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: {'PLP': 1, 'POV': 2} 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: 10.88, per 1000 atoms: 0.59 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: 7.18 Conformation dependent library (CDL) restraints added in 2.7 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: 1.76 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: 5.20 Time building geometry restraints manager: 7.73 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: 1.800 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: 10.320 Check model and map are aligned: 0.260 Process input model: 46.810 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.370 ------------------------------------------------------------------------------- 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 : 2.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 1.6543 time to fit residues: 460.0615 Evaluate side-chains 175 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7932 ------------------------------------------------------------------------------- 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: 0.7886 moved from start: 0.0725 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= 0.185 Angle : 0.485 6.468 25620 Z= 0.252 Chirality : 0.041 0.193 2854 Planarity : 0.004 0.050 3244 Dihedral : 6.890 89.174 2712 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.73 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 212 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.130 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 190 average time/residue: 1.5426 time to fit residues: 324.8819 Evaluate side-chains 183 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.2333 time to fit residues: 8.4777 ------------------------------------------------------------------------------- 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: 1.9990 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 187 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 18964 Z= 0.322 Angle : 0.551 9.378 25620 Z= 0.283 Chirality : 0.044 0.193 2854 Planarity : 0.004 0.053 3244 Dihedral : 6.564 66.453 2712 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2326 helix: 1.68 (0.15), residues: 1140 sheet: 0.23 (0.32), residues: 266 loop : -0.62 (0.20), residues: 920 *********************** 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 221 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 2.162 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 206 average time/residue: 1.5981 time to fit residues: 364.6218 Evaluate side-chains 186 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.5660 time to fit residues: 4.8351 ------------------------------------------------------------------------------- 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: 0.6980 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 100 optimal weight: 50.0000 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 A 407 GLN E 77 HIS E 372 GLN E 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 18964 Z= 0.264 Angle : 0.512 6.485 25620 Z= 0.266 Chirality : 0.043 0.184 2854 Planarity : 0.004 0.051 3244 Dihedral : 6.168 64.556 2712 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.87 (0.18), residues: 2326 helix: 1.61 (0.15), residues: 1152 sheet: 0.19 (0.32), residues: 266 loop : -0.61 (0.20), 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 222 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 2.041 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 205 average time/residue: 1.5775 time to fit residues: 358.8051 Evaluate side-chains 194 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.2892 time to fit residues: 5.0870 ------------------------------------------------------------------------------- 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: 0.4980 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 60.0000 chunk 114 optimal weight: 0.0970 chunk 201 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 85 HIS E 77 HIS E 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18964 Z= 0.183 Angle : 0.465 6.459 25620 Z= 0.243 Chirality : 0.041 0.176 2854 Planarity : 0.004 0.047 3244 Dihedral : 5.802 63.334 2712 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 1.00 (0.18), residues: 2326 helix: 1.75 (0.15), residues: 1162 sheet: 0.13 (0.32), residues: 270 loop : -0.58 (0.21), residues: 894 *********************** 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 226 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 2.200 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 209 average time/residue: 1.5280 time to fit residues: 355.8484 Evaluate side-chains 190 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.5548 time to fit residues: 7.9662 ------------------------------------------------------------------------------- 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: 0.2980 chunk 201 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7911 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18964 Z= 0.215 Angle : 0.483 6.618 25620 Z= 0.251 Chirality : 0.041 0.140 2854 Planarity : 0.004 0.046 3244 Dihedral : 5.781 63.252 2712 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 1.01 (0.18), residues: 2326 helix: 1.79 (0.15), residues: 1150 sheet: -0.00 (0.33), residues: 250 loop : -0.53 (0.20), residues: 926 *********************** 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 209 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 2.190 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 197 average time/residue: 1.5641 time to fit residues: 342.0019 Evaluate side-chains 186 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.3075 time to fit residues: 3.7053 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 0.0770 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 125 optimal weight: 0.0970 chunk 223 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 E 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 18964 Z= 0.124 Angle : 0.435 7.132 25620 Z= 0.226 Chirality : 0.039 0.136 2854 Planarity : 0.004 0.046 3244 Dihedral : 5.440 61.640 2712 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.24 (0.18), residues: 2326 helix: 2.00 (0.16), residues: 1150 sheet: 0.23 (0.32), residues: 270 loop : -0.52 (0.21), residues: 906 *********************** 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 214 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 2.116 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 1.4920 time to fit residues: 343.4056 Evaluate side-chains 187 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.3424 time to fit residues: 5.0031 ------------------------------------------------------------------------------- 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: 1.9990 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.0570 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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 F 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 18964 Z= 0.330 Angle : 0.548 7.069 25620 Z= 0.283 Chirality : 0.044 0.145 2854 Planarity : 0.004 0.047 3244 Dihedral : 5.995 64.040 2712 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.96 % 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: 0.91 (0.18), residues: 2326 helix: 1.75 (0.15), residues: 1138 sheet: 0.01 (0.33), residues: 250 loop : -0.62 (0.20), residues: 938 *********************** 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 220 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 2.347 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 208 average time/residue: 1.6087 time to fit residues: 374.4011 Evaluate side-chains 184 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.3369 time to fit residues: 10.5531 ------------------------------------------------------------------------------- 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: 2.9990 chunk 208 optimal weight: 0.5980 chunk 214 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 136 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 HIS F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1450 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= 0.165 Angle : 0.463 7.743 25620 Z= 0.240 Chirality : 0.040 0.139 2854 Planarity : 0.004 0.047 3244 Dihedral : 5.621 61.912 2712 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 1.24 % 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: 1.09 (0.18), residues: 2326 helix: 1.86 (0.16), residues: 1152 sheet: 0.19 (0.32), residues: 270 loop : -0.57 (0.20), residues: 904 *********************** 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 200 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.167 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 198 average time/residue: 1.4722 time to fit residues: 325.9807 Evaluate side-chains 184 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.3408 time to fit residues: 4.0306 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 231 optimal weight: 0.8980 chunk 212 optimal weight: 0.4980 chunk 184 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18964 Z= 0.124 Angle : 0.440 8.452 25620 Z= 0.226 Chirality : 0.039 0.132 2854 Planarity : 0.004 0.046 3244 Dihedral : 5.256 59.723 2712 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.14 % 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: 2.10 (0.16), residues: 1140 sheet: 0.39 (0.32), residues: 266 loop : -0.53 (0.21), residues: 920 ********************** 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 201 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 2.316 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 199 average time/residue: 1.3526 time to fit residues: 302.0667 Evaluate side-chains 180 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.183 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.2191 time to fit residues: 3.2336 ------------------------------------------------------------------------------- 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: 0.0670 chunk 56 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 51 optimal weight: 0.4980 chunk 184 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.133977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103922 restraints weight = 22725.136| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.46 r_work: 0.3012 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1620 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= 0.131 Angle : 0.441 8.297 25620 Z= 0.226 Chirality : 0.040 0.132 2854 Planarity : 0.004 0.046 3244 Dihedral : 5.149 57.844 2712 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 1.09 % 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: 1.40 (0.18), residues: 2326 helix: 2.15 (0.16), residues: 1140 sheet: 0.41 (0.32), residues: 266 loop : -0.47 (0.21), residues: 920 =============================================================================== Job complete usr+sys time: 6132.11 seconds wall clock time: 109 minutes 52.56 seconds (6592.56 seconds total)