Starting phenix.real_space_refine on Mon Apr 8 15:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/04_2024/8oqa_17110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/04_2024/8oqa_17110.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/8oqa_17110/04_2024/8oqa_17110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/04_2024/8oqa_17110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/04_2024/8oqa_17110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/04_2024/8oqa_17110_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 2 4.86 5 C 9027 2.51 5 N 2177 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2682 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {' CL': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1, 'RI5': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 47 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.37, per 1000 atoms: 0.54 Number of scatterers: 13762 At special positions: 0 Unit cell: (93.03, 95.688, 136.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 75 16.00 O 2481 8.00 N 2177 7.00 C 9027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 603 " - " ASN B 140 " " NAG B 604 " - " ASN B 234 " " NAG C 602 " - " ASN C 140 " " NAG C 603 " - " ASN C 234 " " NAG D 602 " - " ASN D 140 " " NAG D 603 " - " ASN D 234 " " NAG E 503 " - " ASN E 140 " " NAG E 504 " - " ASN E 234 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 30 sheets defined 37.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.835A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 282 through 304 removed outlier: 4.346A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.697A pdb=" N VAL A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 334 Proline residue: A 315 - end of helix removed outlier: 4.411A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 379 Processing helix chain 'A' and resid 454 through 477 removed outlier: 4.061A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 3.561A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' 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 148 through 151 removed outlier: 3.710A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 289 through 304 removed outlier: 3.512A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 334 Proline residue: B 315 - end of helix removed outlier: 4.649A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 379 Processing helix chain 'B' and resid 454 through 477 removed outlier: 4.038A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.613A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 304 removed outlier: 3.821A pdb=" N VAL C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 334 Proline residue: C 315 - end of helix removed outlier: 4.422A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 379 Processing helix chain 'C' and resid 454 through 477 removed outlier: 4.107A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.764A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 282 through 304 removed outlier: 4.384A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.582A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 334 Proline residue: D 315 - end of helix removed outlier: 4.300A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 379 Processing helix chain 'D' and resid 454 through 477 removed outlier: 4.199A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 148 through 151 removed outlier: 3.721A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 148 through 151' Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 282 through 304 removed outlier: 4.289A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.540A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 334 Proline residue: E 315 - end of helix removed outlier: 4.339A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 379 Processing helix chain 'E' and resid 454 through 477 removed outlier: 4.329A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.410A pdb=" N ILE A 97 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N TYR A 229 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 99 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.937A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.662A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 262 Processing sheet with id= F, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.060A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 removed outlier: 6.292A pdb=" N ILE B 97 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR B 229 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 99 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.879A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.771A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 254 through 261 Processing sheet with id= L, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.922A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.255A pdb=" N ILE C 97 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR C 229 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 99 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= O, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.912A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.669A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 262 Processing sheet with id= R, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.976A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.190A pdb=" N ILE D 97 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR D 229 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 99 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.918A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.725A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 254 through 261 Processing sheet with id= X, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.972A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.366A pdb=" N ILE E 97 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR E 229 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 99 " --> pdb=" O TYR E 229 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AA, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.969A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.743A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 254 through 262 Processing sheet with id= AD, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.882A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1911 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: 3.95 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2125 1.32 - 1.45: 4202 1.45 - 1.57: 7648 1.57 - 1.69: 1 1.69 - 1.82: 140 Bond restraints: 14116 Sorted by residual: bond pdb=" C15 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.396 1.447 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " ideal model delta sigma weight residual 1.530 1.487 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C08 RI5 B 610 " pdb=" O20 RI5 B 610 " ideal model delta sigma weight residual 1.395 1.433 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C14 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.419 1.451 -0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" N ABU D 601 " pdb=" CA ABU D 601 " ideal model delta sigma weight residual 1.457 1.485 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 14111 not shown) Histogram of bond angle deviations from ideal: 59.69 - 74.56: 3 74.56 - 89.43: 0 89.43 - 104.30: 205 104.30 - 119.17: 11384 119.17 - 134.04: 7573 Bond angle restraints: 19165 Sorted by residual: angle pdb=" N ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.86 115.88 -5.02 1.60e+00 3.91e-01 9.85e+00 angle pdb=" C ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.98 106.61 4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 108.60 5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 108.98 4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " pdb=" CD1 ILE E 341 " ideal model delta sigma weight residual 113.80 108.13 5.67 2.10e+00 2.27e-01 7.29e+00 ... (remaining 19160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7973 17.57 - 35.14: 368 35.14 - 52.71: 54 52.71 - 70.28: 10 70.28 - 87.84: 5 Dihedral angle restraints: 8410 sinusoidal: 3485 harmonic: 4925 Sorted by residual: dihedral pdb=" CA LEU C 108 " pdb=" C LEU C 108 " pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN B 251 " pdb=" C GLN B 251 " pdb=" N GLU B 252 " pdb=" CA GLU B 252 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU B 108 " pdb=" C LEU B 108 " pdb=" N ASP B 109 " pdb=" CA ASP B 109 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2187 0.149 - 0.298: 1 0.298 - 0.447: 3 0.447 - 0.597: 2 0.597 - 0.746: 4 Chirality restraints: 2197 Sorted by residual: chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 140 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -3.12 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 140 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -3.11 0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 2194 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.007 2.00e-02 2.50e+03 3.52e-01 1.55e+03 pdb=" CG ASN B 234 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.282 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.605 2.00e-02 2.50e+03 pdb=" C1 NAG B 604 " 0.408 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.230 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" CG ASN C 234 " 0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.515 2.00e-02 2.50e+03 pdb=" C1 NAG C 603 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.273 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" CG ASN A 234 " -0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.466 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " 0.388 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 87 2.64 - 3.20: 11434 3.20 - 3.77: 19802 3.77 - 4.33: 29516 4.33 - 4.90: 48762 Nonbonded interactions: 109601 Sorted by model distance: nonbonded pdb=" CB ASN B 140 " pdb=" O5 NAG B 603 " model vdw 2.070 3.440 nonbonded pdb=" O PRO D 315 " pdb=" OG1 THR D 319 " model vdw 2.198 2.440 nonbonded pdb=" ND2 ASN D 332 " pdb=" OE1 GLN E 287 " model vdw 2.232 2.520 nonbonded pdb=" CD2 HIS C 254 " pdb=" O6 NAG C 603 " model vdw 2.252 2.608 nonbonded pdb=" O VAL B 296 " pdb=" OG SER B 299 " model vdw 2.264 2.440 ... (remaining 109596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 372 or (resid 373 through 451 and (name N or na \ me CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'B' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 251 or (resid 252 and (name N or n \ ame CA or name C or name O or name CB )) or resid 253 through 374 or (resid 375 \ through 451 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 2 through 479)) selection = (chain 'C' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'D' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'E' and (resid 80 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O or name CB )) or resid 253 through 371 or (resid 372 through 451 a \ nd (name N or name CA or name C or name O or name CB )) or resid 452 through 479 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.080 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: 15.310 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.210 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.003 0.051 14116 Z= 0.181 Angle : 0.592 9.179 19165 Z= 0.306 Chirality : 0.056 0.746 2197 Planarity : 0.004 0.031 2334 Dihedral : 10.525 87.844 5207 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.61 % Allowed : 3.97 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 575 sheet: 1.44 (0.24), residues: 455 loop : 0.75 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 349 HIS 0.002 0.001 HIS E 254 PHE 0.017 0.001 PHE E 290 TYR 0.022 0.001 TYR C 362 ARG 0.006 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 349 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.7357 (mmm) cc_final: 0.7109 (mmt) REVERT: B 82 ASP cc_start: 0.6502 (m-30) cc_final: 0.6152 (p0) REVERT: B 83 ASP cc_start: 0.7157 (m-30) cc_final: 0.6918 (m-30) REVERT: B 116 MET cc_start: 0.8120 (mtt) cc_final: 0.7861 (mtm) REVERT: B 117 ASP cc_start: 0.7805 (p0) cc_final: 0.7514 (p0) REVERT: B 223 GLU cc_start: 0.7577 (pt0) cc_final: 0.7304 (pp20) REVERT: B 258 LYS cc_start: 0.8000 (tttt) cc_final: 0.7755 (ttpt) REVERT: C 143 MET cc_start: 0.7568 (mmm) cc_final: 0.7156 (mmp) REVERT: D 304 TRP cc_start: 0.8146 (m100) cc_final: 0.7926 (m-90) REVERT: D 326 THR cc_start: 0.8469 (m) cc_final: 0.8156 (p) REVERT: D 337 ARG cc_start: 0.6283 (mtt180) cc_final: 0.5930 (mtp-110) REVERT: E 102 ASP cc_start: 0.7733 (t0) cc_final: 0.7382 (t0) REVERT: E 232 LYS cc_start: 0.7543 (mttt) cc_final: 0.7038 (mtpp) REVERT: E 295 MET cc_start: 0.8136 (mmm) cc_final: 0.7390 (mmt) outliers start: 9 outliers final: 6 residues processed: 356 average time/residue: 1.3423 time to fit residues: 519.3626 Evaluate side-chains 265 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 210 GLN A 287 GLN B 210 GLN B 247 GLN B 332 ASN C 269 ASN D 251 GLN D 287 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14116 Z= 0.407 Angle : 0.764 9.508 19165 Z= 0.408 Chirality : 0.059 1.057 2197 Planarity : 0.006 0.053 2334 Dihedral : 8.206 76.168 2175 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.98 % Allowed : 12.12 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.15 (0.20), residues: 1630 helix: 1.29 (0.21), residues: 610 sheet: 0.99 (0.23), residues: 490 loop : 0.05 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 349 HIS 0.007 0.002 HIS E 126 PHE 0.024 0.003 PHE A 356 TYR 0.026 0.003 TYR E 362 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 245 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.7243 (mmm) cc_final: 0.6938 (mmt) REVERT: A 183 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7359 (p0) REVERT: A 269 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7589 (m-40) REVERT: B 82 ASP cc_start: 0.6746 (m-30) cc_final: 0.6310 (p0) REVERT: B 117 ASP cc_start: 0.7823 (p0) cc_final: 0.7440 (p0) REVERT: C 143 MET cc_start: 0.7462 (mmm) cc_final: 0.7080 (mmp) REVERT: C 258 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7484 (ttpp) REVERT: D 287 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6752 (mp-120) REVERT: D 350 VAL cc_start: 0.8376 (t) cc_final: 0.8140 (t) REVERT: E 232 LYS cc_start: 0.7626 (mttt) cc_final: 0.7143 (mtpp) outliers start: 74 outliers final: 42 residues processed: 289 average time/residue: 1.3991 time to fit residues: 445.0392 Evaluate side-chains 277 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN D 251 GLN D 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14116 Z= 0.213 Angle : 0.598 8.272 19165 Z= 0.320 Chirality : 0.046 0.485 2197 Planarity : 0.004 0.035 2334 Dihedral : 7.474 77.099 2173 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.04 % Allowed : 14.81 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.41 (0.20), residues: 1630 helix: 1.63 (0.22), residues: 610 sheet: 1.19 (0.24), residues: 445 loop : 0.06 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.017 0.002 PHE E 356 TYR 0.021 0.002 TYR E 362 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 239 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7230 (p0) REVERT: A 235 ASP cc_start: 0.6909 (p0) cc_final: 0.6544 (t70) REVERT: A 269 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7416 (m-40) REVERT: A 334 SER cc_start: 0.4519 (OUTLIER) cc_final: 0.4250 (p) REVERT: B 82 ASP cc_start: 0.6743 (m-30) cc_final: 0.6324 (p0) REVERT: B 108 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 117 ASP cc_start: 0.7804 (p0) cc_final: 0.7412 (p0) REVERT: C 143 MET cc_start: 0.7380 (mmm) cc_final: 0.6987 (mmp) REVERT: C 151 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7864 (mmpt) REVERT: D 241 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6621 (tp30) REVERT: E 232 LYS cc_start: 0.7477 (mttt) cc_final: 0.7035 (mtpp) REVERT: E 295 MET cc_start: 0.8098 (mmm) cc_final: 0.7765 (mmp) REVERT: E 456 ASP cc_start: 0.7507 (m-30) cc_final: 0.6916 (m-30) outliers start: 60 outliers final: 28 residues processed: 276 average time/residue: 1.3307 time to fit residues: 401.7919 Evaluate side-chains 262 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 247 GLN D 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14116 Z= 0.221 Angle : 0.594 10.447 19165 Z= 0.318 Chirality : 0.046 0.469 2197 Planarity : 0.004 0.033 2334 Dihedral : 7.237 77.164 2173 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.92 % Allowed : 15.15 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.39 (0.21), residues: 1630 helix: 1.71 (0.22), residues: 610 sheet: 1.03 (0.24), residues: 475 loop : 0.02 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 349 HIS 0.006 0.001 HIS C 254 PHE 0.017 0.002 PHE A 356 TYR 0.024 0.002 TYR B 362 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 235 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.5374 (OUTLIER) cc_final: 0.5154 (t0) REVERT: A 183 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7210 (p0) REVERT: A 235 ASP cc_start: 0.7001 (p0) cc_final: 0.6550 (t70) REVERT: A 269 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7405 (m-40) REVERT: B 82 ASP cc_start: 0.6806 (m-30) cc_final: 0.6352 (p0) REVERT: B 108 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 117 ASP cc_start: 0.7795 (p0) cc_final: 0.7414 (p0) REVERT: B 223 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: C 143 MET cc_start: 0.7281 (mmm) cc_final: 0.6965 (mmp) REVERT: C 151 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7901 (mmpt) REVERT: C 258 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (tttp) REVERT: D 241 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6565 (tp30) REVERT: E 232 LYS cc_start: 0.7483 (mttt) cc_final: 0.7049 (mtpp) REVERT: E 295 MET cc_start: 0.8105 (mmm) cc_final: 0.7769 (mmp) REVERT: E 456 ASP cc_start: 0.7527 (m-30) cc_final: 0.6898 (m-30) REVERT: E 457 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7498 (ttpp) outliers start: 73 outliers final: 38 residues processed: 280 average time/residue: 1.2699 time to fit residues: 388.5733 Evaluate side-chains 275 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN D 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14116 Z= 0.345 Angle : 0.679 7.537 19165 Z= 0.364 Chirality : 0.049 0.452 2197 Planarity : 0.005 0.037 2334 Dihedral : 7.675 78.036 2173 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.86 % Allowed : 15.22 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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 (0.20), residues: 1630 helix: 1.44 (0.22), residues: 605 sheet: 1.13 (0.24), residues: 435 loop : -0.36 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 349 HIS 0.007 0.002 HIS C 254 PHE 0.022 0.002 PHE A 356 TYR 0.026 0.002 TYR B 362 ARG 0.004 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 226 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7327 (p0) REVERT: A 235 ASP cc_start: 0.7099 (p0) cc_final: 0.6630 (t70) REVERT: A 269 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (m-40) REVERT: B 82 ASP cc_start: 0.6868 (m-30) cc_final: 0.6374 (p0) REVERT: B 108 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 117 ASP cc_start: 0.7736 (p0) cc_final: 0.7329 (p0) REVERT: C 102 ASP cc_start: 0.7802 (m-30) cc_final: 0.7474 (m-30) REVERT: C 143 MET cc_start: 0.7336 (mmm) cc_final: 0.6980 (mmp) REVERT: C 151 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7830 (mmpt) REVERT: C 258 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7967 (tttp) REVERT: D 241 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6538 (tp30) REVERT: D 350 VAL cc_start: 0.8374 (t) cc_final: 0.8127 (t) REVERT: E 232 LYS cc_start: 0.7617 (mttt) cc_final: 0.7177 (mtpp) REVERT: E 457 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7429 (ttpp) outliers start: 87 outliers final: 51 residues processed: 279 average time/residue: 1.2472 time to fit residues: 380.7051 Evaluate side-chains 282 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 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 210 GLN A 287 GLN B 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14116 Z= 0.174 Angle : 0.563 14.951 19165 Z= 0.297 Chirality : 0.046 0.536 2197 Planarity : 0.004 0.034 2334 Dihedral : 7.159 77.523 2173 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.04 % Allowed : 17.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.46 (0.20), residues: 1630 helix: 1.74 (0.22), residues: 610 sheet: 1.41 (0.24), residues: 430 loop : -0.13 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 349 HIS 0.004 0.001 HIS C 254 PHE 0.016 0.001 PHE E 356 TYR 0.021 0.002 TYR B 362 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 229 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7061 (p0) cc_final: 0.6591 (t70) REVERT: A 269 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: B 82 ASP cc_start: 0.6870 (m-30) cc_final: 0.6396 (p0) REVERT: B 117 ASP cc_start: 0.7738 (p0) cc_final: 0.7346 (p0) REVERT: B 223 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: C 108 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8356 (tt) REVERT: C 143 MET cc_start: 0.7204 (mmm) cc_final: 0.6854 (mmp) REVERT: C 151 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7891 (mmpt) REVERT: C 258 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7973 (tttp) REVERT: D 241 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6557 (tp30) REVERT: D 278 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7448 (tpp-160) REVERT: E 227 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6679 (tmt) REVERT: E 232 LYS cc_start: 0.7483 (mttt) cc_final: 0.7053 (mtpp) REVERT: E 295 MET cc_start: 0.8088 (mmm) cc_final: 0.7684 (mmp) REVERT: E 456 ASP cc_start: 0.7509 (m-30) cc_final: 0.6884 (m-30) REVERT: E 457 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7195 (mtpp) outliers start: 60 outliers final: 35 residues processed: 266 average time/residue: 1.2661 time to fit residues: 368.6448 Evaluate side-chains 263 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN B 247 GLN D 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14116 Z= 0.243 Angle : 0.601 8.579 19165 Z= 0.320 Chirality : 0.046 0.431 2197 Planarity : 0.004 0.035 2334 Dihedral : 8.440 117.684 2171 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.58 % Allowed : 17.37 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.33 (0.20), residues: 1630 helix: 1.65 (0.22), residues: 610 sheet: 1.28 (0.24), residues: 435 loop : -0.19 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 349 HIS 0.006 0.001 HIS C 254 PHE 0.018 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 226 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7264 (p0) REVERT: A 235 ASP cc_start: 0.7099 (p0) cc_final: 0.6642 (t70) REVERT: A 269 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7345 (m-40) REVERT: B 82 ASP cc_start: 0.6922 (m-30) cc_final: 0.6400 (p0) REVERT: B 117 ASP cc_start: 0.7738 (p0) cc_final: 0.7342 (p0) REVERT: B 223 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6955 (pp20) REVERT: C 102 ASP cc_start: 0.7753 (m-30) cc_final: 0.7423 (m-30) REVERT: C 108 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8415 (tt) REVERT: C 143 MET cc_start: 0.7290 (mmm) cc_final: 0.6951 (mmp) REVERT: C 151 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7900 (mmpt) REVERT: C 258 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7972 (tttp) REVERT: D 241 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6549 (tp30) REVERT: D 278 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7388 (tpp-160) REVERT: E 232 LYS cc_start: 0.7549 (mttt) cc_final: 0.7130 (mtpp) REVERT: E 295 MET cc_start: 0.8096 (mmm) cc_final: 0.7718 (mmp) REVERT: E 456 ASP cc_start: 0.7572 (m-30) cc_final: 0.6957 (m-30) REVERT: E 457 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7424 (ttpp) outliers start: 68 outliers final: 47 residues processed: 271 average time/residue: 1.2980 time to fit residues: 384.6713 Evaluate side-chains 275 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 220 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN B 247 GLN C 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14116 Z= 0.205 Angle : 0.568 7.817 19165 Z= 0.304 Chirality : 0.045 0.421 2197 Planarity : 0.004 0.034 2334 Dihedral : 8.216 119.278 2171 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.44 % Allowed : 17.98 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.44 (0.20), residues: 1630 helix: 1.72 (0.22), residues: 610 sheet: 1.40 (0.24), residues: 430 loop : -0.15 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.019 0.002 PHE E 356 TYR 0.022 0.002 TYR B 362 ARG 0.003 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 221 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7232 (p0) REVERT: A 235 ASP cc_start: 0.7049 (p0) cc_final: 0.6601 (t70) REVERT: A 269 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7297 (m-40) REVERT: B 82 ASP cc_start: 0.6918 (m-30) cc_final: 0.6401 (p0) REVERT: B 117 ASP cc_start: 0.7732 (p0) cc_final: 0.7345 (p0) REVERT: B 223 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: C 108 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8383 (tt) REVERT: C 143 MET cc_start: 0.7300 (mmm) cc_final: 0.6967 (mmp) REVERT: C 151 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7908 (mmpt) REVERT: C 258 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8005 (tttp) REVERT: D 241 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6594 (tp30) REVERT: D 278 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7453 (tpp-160) REVERT: D 287 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6178 (mp10) REVERT: E 232 LYS cc_start: 0.7535 (mttt) cc_final: 0.7119 (mtpp) REVERT: E 295 MET cc_start: 0.8106 (mmm) cc_final: 0.7714 (mmp) REVERT: E 456 ASP cc_start: 0.7541 (m-30) cc_final: 0.6916 (m-30) REVERT: E 457 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7212 (mtpp) outliers start: 66 outliers final: 49 residues processed: 265 average time/residue: 1.2519 time to fit residues: 363.2391 Evaluate side-chains 277 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.0570 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN B 247 GLN C 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14116 Z= 0.196 Angle : 0.549 7.731 19165 Z= 0.294 Chirality : 0.044 0.412 2197 Planarity : 0.004 0.034 2334 Dihedral : 8.008 119.018 2171 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.44 % Allowed : 18.05 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.50 (0.21), residues: 1630 helix: 1.81 (0.22), residues: 610 sheet: 1.42 (0.24), residues: 430 loop : -0.16 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.019 0.002 PHE E 356 TYR 0.021 0.002 TYR B 362 ARG 0.002 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 223 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7152 (p0) REVERT: A 235 ASP cc_start: 0.7077 (p0) cc_final: 0.6628 (t70) REVERT: A 269 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7271 (m-40) REVERT: B 82 ASP cc_start: 0.6930 (m-30) cc_final: 0.6405 (p0) REVERT: B 117 ASP cc_start: 0.7714 (p0) cc_final: 0.7336 (p0) REVERT: B 223 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: B 249 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7654 (tp) REVERT: C 108 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8353 (tt) REVERT: C 143 MET cc_start: 0.7320 (mmm) cc_final: 0.6995 (mmp) REVERT: C 151 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7868 (mmpt) REVERT: C 472 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7309 (mp) REVERT: C 477 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7811 (mt) REVERT: D 241 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6596 (tp30) REVERT: D 278 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7442 (tpp-160) REVERT: E 232 LYS cc_start: 0.7482 (mttt) cc_final: 0.7084 (mtpp) REVERT: E 295 MET cc_start: 0.8094 (mmm) cc_final: 0.7686 (mmp) REVERT: E 456 ASP cc_start: 0.7500 (m-30) cc_final: 0.6849 (m-30) REVERT: E 457 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7199 (mtpp) outliers start: 66 outliers final: 47 residues processed: 267 average time/residue: 1.2397 time to fit residues: 362.9332 Evaluate side-chains 278 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN D 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14116 Z= 0.259 Angle : 0.606 6.978 19165 Z= 0.326 Chirality : 0.046 0.423 2197 Planarity : 0.004 0.035 2334 Dihedral : 8.359 119.471 2171 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.11 % Allowed : 18.32 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.29 (0.20), residues: 1630 helix: 1.62 (0.22), residues: 610 sheet: 1.33 (0.24), residues: 430 loop : -0.27 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 349 HIS 0.006 0.001 HIS C 254 PHE 0.019 0.002 PHE A 356 TYR 0.024 0.002 TYR E 362 ARG 0.003 0.000 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7081 (p0) cc_final: 0.6664 (t70) REVERT: A 269 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: B 82 ASP cc_start: 0.6900 (m-30) cc_final: 0.6391 (p0) REVERT: B 117 ASP cc_start: 0.7725 (p0) cc_final: 0.7318 (p0) REVERT: C 102 ASP cc_start: 0.7761 (m-30) cc_final: 0.7451 (m-30) REVERT: C 108 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8448 (tt) REVERT: C 143 MET cc_start: 0.7368 (mmm) cc_final: 0.7013 (mmp) REVERT: C 151 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7901 (mmpt) REVERT: D 241 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6552 (tp30) REVERT: D 278 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7403 (tpp-160) REVERT: E 232 LYS cc_start: 0.7590 (mttt) cc_final: 0.7166 (mtpp) REVERT: E 295 MET cc_start: 0.8102 (mmm) cc_final: 0.7760 (mmp) REVERT: E 457 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7210 (mtpp) outliers start: 61 outliers final: 50 residues processed: 264 average time/residue: 1.2565 time to fit residues: 362.6685 Evaluate side-chains 277 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 222 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 0.0050 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.105054 restraints weight = 16202.685| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.73 r_work: 0.2984 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14116 Z= 0.211 Angle : 0.563 7.354 19165 Z= 0.302 Chirality : 0.045 0.416 2197 Planarity : 0.004 0.034 2334 Dihedral : 8.163 118.300 2171 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.91 % Allowed : 18.52 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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 (0.20), residues: 1630 helix: 1.74 (0.22), residues: 610 sheet: 1.37 (0.24), residues: 430 loop : -0.22 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.018 0.002 PHE E 356 TYR 0.021 0.002 TYR E 362 ARG 0.002 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5979.45 seconds wall clock time: 111 minutes 18.83 seconds (6678.83 seconds total)