Starting phenix.real_space_refine on Fri Aug 9 00:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/08_2024/8tz7_41736_trim.cif" } resolution = 3.0 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= 0.002 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 87 5.16 5 C 8187 2.51 5 N 1923 2.21 5 O 2139 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 11.58, per 1000 atoms: 0.47 Number of scatterers: 24408 At special positions: 0 Unit cell: (128.52, 128.52, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 3 15.00 O 2139 8.00 N 1923 7.00 C 8187 6.00 H 12069 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.93 Conformation dependent library (CDL) restraints added in 3.4 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 90 through 130 removed outlier: 5.832A pdb=" N THR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.714A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.760A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.442A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.513A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.404A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.831A pdb=" N VAL A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.637A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 4.058A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.083A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.590A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 130 removed outlier: 5.832A pdb=" N THR B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.714A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.761A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.441A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.514A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.403A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.832A pdb=" N VAL B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.637A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 4.059A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.083A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.589A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 596 Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 130 removed outlier: 5.833A pdb=" N THR C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 203 Proline residue: C 167 - end of helix removed outlier: 4.713A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.761A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.441A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.513A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.404A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.831A pdb=" N VAL C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.636A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.059A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.084A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 481 removed outlier: 3.706A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.590A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.274A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.988A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 596 Processing helix chain 'C' and resid 596 through 619 removed outlier: 3.548A pdb=" N LEU C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 602 " --> pdb=" O MET C 598 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2856 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: 8.52 Time building geometry restraints manager: 21.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12051 1.03 - 1.23: 31 1.23 - 1.42: 5345 1.42 - 1.62: 7149 1.62 - 1.81: 165 Bond restraints: 24741 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.683 -0.285 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.682 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.681 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.291 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.291 0.243 2.00e-02 2.50e+03 1.47e+02 ... (remaining 24736 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 412 106.60 - 113.46: 28485 113.46 - 120.32: 8460 120.32 - 127.18: 7038 127.18 - 134.05: 164 Bond angle restraints: 44559 Sorted by residual: angle pdb=" O1 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O2 LBN C 802 " ideal model delta sigma weight residual 93.45 109.34 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN B 802 " pdb=" P1 LBN B 802 " pdb=" O2 LBN B 802 " ideal model delta sigma weight residual 93.45 109.32 -15.87 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.30 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.85 4.34 1.29e+00 6.01e-01 1.13e+01 angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 103.89 4.30 1.29e+00 6.01e-01 1.11e+01 ... (remaining 44554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 11314 26.60 - 53.21: 406 53.21 - 79.81: 106 79.81 - 106.41: 6 106.41 - 133.02: 3 Dihedral angle restraints: 11835 sinusoidal: 6105 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 802 " pdb=" C2 LBN A 802 " pdb=" C3 LBN A 802 " pdb=" O7 LBN A 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.31 -133.02 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN C 802 " pdb=" C2 LBN C 802 " pdb=" C3 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.35 -132.98 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN B 802 " pdb=" C2 LBN B 802 " pdb=" C3 LBN B 802 " pdb=" O7 LBN B 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.36 -132.97 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 11832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1756 0.067 - 0.134: 230 0.134 - 0.202: 0 0.202 - 0.269: 0 0.269 - 0.336: 3 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.41 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1986 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO C 296 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 296 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 296 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.024 5.00e-02 4.00e+02 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 486 2.13 - 2.75: 42845 2.75 - 3.36: 69920 3.36 - 3.98: 86051 3.98 - 4.60: 139144 Nonbonded interactions: 338446 Sorted by model distance: nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.511 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.513 2.450 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.513 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.559 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.560 2.450 ... (remaining 338441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.630 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: 0.390 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 80.270 Find NCS groups from input model: 0.660 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.010 0.285 12672 Z= 0.615 Angle : 0.682 15.886 17241 Z= 0.330 Chirality : 0.040 0.336 1989 Planarity : 0.003 0.044 2091 Dihedral : 12.773 133.018 4365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.21), residues: 1593 helix: 2.94 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE B 488 TYR 0.007 0.001 TYR B 519 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6891 (tp) cc_final: 0.6669 (mt) REVERT: A 307 MET cc_start: 0.8471 (mtm) cc_final: 0.8098 (mtp) REVERT: A 497 MET cc_start: 0.7792 (tmt) cc_final: 0.6777 (tmt) REVERT: A 598 MET cc_start: 0.8202 (tpp) cc_final: 0.7635 (tpt) REVERT: B 307 MET cc_start: 0.8419 (mtm) cc_final: 0.8215 (mtp) REVERT: B 329 MET cc_start: 0.8462 (mtp) cc_final: 0.8238 (mtm) REVERT: C 329 MET cc_start: 0.8538 (mtp) cc_final: 0.8160 (mtm) REVERT: C 344 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p90) REVERT: C 430 MET cc_start: 0.8057 (mtt) cc_final: 0.7540 (mtt) REVERT: C 497 MET cc_start: 0.7517 (tmt) cc_final: 0.7170 (tmt) outliers start: 6 outliers final: 2 residues processed: 239 average time/residue: 1.5793 time to fit residues: 432.2731 Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12672 Z= 0.162 Angle : 0.480 4.620 17241 Z= 0.256 Chirality : 0.036 0.126 1989 Planarity : 0.003 0.040 2091 Dihedral : 9.148 140.857 1860 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.36 % Allowed : 9.86 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.004 0.001 HIS B 288 PHE 0.013 0.001 PHE A 523 TYR 0.006 0.001 TYR A 309 ARG 0.003 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6768 (tp) cc_final: 0.6562 (mp) REVERT: A 307 MET cc_start: 0.8509 (mtm) cc_final: 0.8171 (mtp) REVERT: A 497 MET cc_start: 0.8010 (tmt) cc_final: 0.6952 (tmt) REVERT: A 598 MET cc_start: 0.8308 (tpp) cc_final: 0.7692 (tpt) REVERT: B 307 MET cc_start: 0.8475 (mtm) cc_final: 0.8272 (mtp) REVERT: B 482 ASP cc_start: 0.8023 (t0) cc_final: 0.7796 (m-30) REVERT: B 497 MET cc_start: 0.8010 (tmt) cc_final: 0.7113 (tmt) REVERT: C 129 MET cc_start: 0.7589 (mtp) cc_final: 0.7222 (mtp) REVERT: C 329 MET cc_start: 0.8806 (mtp) cc_final: 0.8412 (mtm) REVERT: C 344 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (p90) REVERT: C 497 MET cc_start: 0.7888 (tmt) cc_final: 0.7257 (tmt) outliers start: 17 outliers final: 5 residues processed: 188 average time/residue: 1.5671 time to fit residues: 341.2813 Evaluate side-chains 155 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 435 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS B 394 HIS B 508 GLN C 426 ASN C 508 GLN C 571 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12672 Z= 0.286 Angle : 0.523 4.564 17241 Z= 0.286 Chirality : 0.038 0.115 1989 Planarity : 0.004 0.051 2091 Dihedral : 9.205 145.548 1860 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.92 % Allowed : 12.10 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.21), residues: 1593 helix: 2.36 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -1.14 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 323 HIS 0.004 0.001 HIS B 226 PHE 0.018 0.002 PHE B 413 TYR 0.009 0.001 TYR C 494 ARG 0.004 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.833 Fit side-chains REVERT: A 248 LEU cc_start: 0.7205 (tp) cc_final: 0.6915 (mp) REVERT: A 497 MET cc_start: 0.8002 (tmt) cc_final: 0.6960 (tmt) REVERT: A 598 MET cc_start: 0.8454 (tpp) cc_final: 0.7778 (tpt) REVERT: B 284 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7700 (mtpp) REVERT: B 307 MET cc_start: 0.8446 (mtm) cc_final: 0.8215 (mtp) REVERT: B 482 ASP cc_start: 0.8092 (t0) cc_final: 0.7771 (m-30) REVERT: B 497 MET cc_start: 0.8029 (tmt) cc_final: 0.7065 (tmt) REVERT: C 141 THR cc_start: 0.7966 (m) cc_final: 0.7729 (p) REVERT: C 329 MET cc_start: 0.8757 (mtp) cc_final: 0.8528 (mtm) REVERT: C 344 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (p90) REVERT: C 470 MET cc_start: 0.7774 (ttm) cc_final: 0.7572 (ttm) REVERT: C 480 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7616 (mtt) outliers start: 24 outliers final: 13 residues processed: 195 average time/residue: 1.7574 time to fit residues: 389.4318 Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12672 Z= 0.240 Angle : 0.486 4.542 17241 Z= 0.261 Chirality : 0.036 0.115 1989 Planarity : 0.004 0.049 2091 Dihedral : 8.925 142.236 1860 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.24 % Allowed : 14.50 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.21), residues: 1593 helix: 2.33 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -1.26 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS C 226 PHE 0.015 0.001 PHE C 413 TYR 0.008 0.001 TYR C 494 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7241 (tp) cc_final: 0.6941 (mp) REVERT: A 344 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8287 (p90) REVERT: A 497 MET cc_start: 0.8041 (tmt) cc_final: 0.7030 (tmt) REVERT: A 598 MET cc_start: 0.8504 (tpp) cc_final: 0.7850 (tpt) REVERT: B 482 ASP cc_start: 0.8149 (t0) cc_final: 0.7810 (m-30) REVERT: C 329 MET cc_start: 0.8779 (mtp) cc_final: 0.8566 (mtm) REVERT: C 344 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8496 (p90) REVERT: C 470 MET cc_start: 0.7799 (ttm) cc_final: 0.7586 (ttm) REVERT: C 480 MET cc_start: 0.7987 (mmm) cc_final: 0.7630 (mtt) REVERT: C 497 MET cc_start: 0.7978 (tmt) cc_final: 0.6810 (tmt) REVERT: C 583 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (t) outliers start: 28 outliers final: 12 residues processed: 184 average time/residue: 1.7691 time to fit residues: 368.1348 Evaluate side-chains 180 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 205 GLN B 508 GLN C 394 HIS C 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12672 Z= 0.363 Angle : 0.552 4.815 17241 Z= 0.300 Chirality : 0.039 0.126 1989 Planarity : 0.005 0.062 2091 Dihedral : 9.075 148.220 1858 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.21), residues: 1593 helix: 1.93 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS B 226 PHE 0.016 0.002 PHE B 413 TYR 0.010 0.002 TYR C 119 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7527 (tp) cc_final: 0.7212 (mp) REVERT: A 344 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8262 (p90) REVERT: A 497 MET cc_start: 0.8036 (tmt) cc_final: 0.6918 (tmt) REVERT: A 598 MET cc_start: 0.8513 (tpp) cc_final: 0.7811 (tpt) REVERT: B 205 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: B 284 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7662 (mtpp) REVERT: B 470 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7468 (ttp) REVERT: B 482 ASP cc_start: 0.8128 (t0) cc_final: 0.7804 (m-30) REVERT: B 497 MET cc_start: 0.8058 (tmt) cc_final: 0.7052 (tmt) REVERT: C 470 MET cc_start: 0.7792 (ttm) cc_final: 0.7581 (ttm) REVERT: C 480 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7760 (mtt) REVERT: C 497 MET cc_start: 0.7969 (tmt) cc_final: 0.6839 (tmt) REVERT: C 583 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8470 (t) outliers start: 32 outliers final: 15 residues processed: 186 average time/residue: 1.8303 time to fit residues: 386.0969 Evaluate side-chains 180 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 127 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12672 Z= 0.157 Angle : 0.448 4.406 17241 Z= 0.239 Chirality : 0.034 0.113 1989 Planarity : 0.004 0.051 2091 Dihedral : 8.496 141.270 1856 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.44 % Allowed : 15.87 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.21), residues: 1593 helix: 2.35 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.13 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 323 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE C 413 TYR 0.005 0.001 TYR B 216 ARG 0.001 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7211 (tp) cc_final: 0.6944 (mp) REVERT: A 344 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8310 (p90) REVERT: A 497 MET cc_start: 0.8013 (tmt) cc_final: 0.6942 (tmt) REVERT: A 598 MET cc_start: 0.8556 (tpp) cc_final: 0.7898 (tpt) REVERT: B 284 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: B 329 MET cc_start: 0.8890 (mtp) cc_final: 0.8603 (mtp) REVERT: B 482 ASP cc_start: 0.8123 (t0) cc_final: 0.7819 (m-30) REVERT: C 583 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8496 (t) outliers start: 18 outliers final: 8 residues processed: 181 average time/residue: 1.8806 time to fit residues: 383.5800 Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN A 620 ASN B 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12672 Z= 0.222 Angle : 0.471 4.467 17241 Z= 0.251 Chirality : 0.035 0.111 1989 Planarity : 0.004 0.053 2091 Dihedral : 8.495 142.469 1856 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 15.54 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1593 helix: 2.32 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 178 HIS 0.003 0.001 HIS B 226 PHE 0.014 0.001 PHE B 413 TYR 0.006 0.001 TYR C 119 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7304 (tp) cc_final: 0.7025 (mp) REVERT: A 344 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8278 (p90) REVERT: A 497 MET cc_start: 0.8034 (tmt) cc_final: 0.6957 (tmt) REVERT: A 598 MET cc_start: 0.8591 (tpp) cc_final: 0.7913 (tpt) REVERT: B 284 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7558 (mtpp) REVERT: B 329 MET cc_start: 0.8932 (mtp) cc_final: 0.8641 (mtp) REVERT: B 482 ASP cc_start: 0.8125 (t0) cc_final: 0.7820 (m-30) REVERT: B 583 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (t) REVERT: C 583 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8486 (t) outliers start: 24 outliers final: 12 residues processed: 181 average time/residue: 1.8264 time to fit residues: 373.2019 Evaluate side-chains 180 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12672 Z= 0.226 Angle : 0.474 4.936 17241 Z= 0.252 Chirality : 0.035 0.112 1989 Planarity : 0.004 0.054 2091 Dihedral : 8.392 142.142 1856 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.44 % Allowed : 16.35 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.21), residues: 1593 helix: 2.30 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 178 HIS 0.003 0.001 HIS C 226 PHE 0.014 0.001 PHE B 413 TYR 0.006 0.001 TYR A 119 ARG 0.002 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7306 (tp) cc_final: 0.7043 (mp) REVERT: A 497 MET cc_start: 0.8032 (tmt) cc_final: 0.6959 (tmt) REVERT: A 598 MET cc_start: 0.8589 (tpp) cc_final: 0.7906 (tpt) REVERT: B 284 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7543 (mtpp) REVERT: B 482 ASP cc_start: 0.8136 (t0) cc_final: 0.7826 (m-30) REVERT: B 583 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 497 MET cc_start: 0.7954 (tmt) cc_final: 0.6845 (tmt) REVERT: C 583 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8518 (t) outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 1.7695 time to fit residues: 360.7605 Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12672 Z= 0.215 Angle : 0.468 4.459 17241 Z= 0.249 Chirality : 0.035 0.111 1989 Planarity : 0.004 0.053 2091 Dihedral : 8.286 141.300 1854 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.36 % Allowed : 16.75 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1593 helix: 2.32 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.12 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE B 413 TYR 0.006 0.001 TYR A 309 ARG 0.001 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7285 (tp) cc_final: 0.7037 (mp) REVERT: A 497 MET cc_start: 0.8031 (tmt) cc_final: 0.6960 (tmt) REVERT: A 598 MET cc_start: 0.8589 (tpp) cc_final: 0.7901 (tpt) REVERT: B 189 LEU cc_start: 0.8481 (tm) cc_final: 0.8148 (tt) REVERT: B 284 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7549 (mtpp) REVERT: B 482 ASP cc_start: 0.8134 (t0) cc_final: 0.7831 (m-30) REVERT: B 583 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 497 MET cc_start: 0.7956 (tmt) cc_final: 0.6788 (tmt) REVERT: C 583 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8518 (t) outliers start: 17 outliers final: 13 residues processed: 176 average time/residue: 1.7843 time to fit residues: 356.0599 Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12672 Z= 0.210 Angle : 0.467 4.460 17241 Z= 0.248 Chirality : 0.035 0.112 1989 Planarity : 0.004 0.053 2091 Dihedral : 8.227 140.573 1854 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.52 % Allowed : 16.83 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.21), residues: 1593 helix: 2.33 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE C 413 TYR 0.005 0.001 TYR C 119 ARG 0.001 0.000 ARG C 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7282 (tp) cc_final: 0.7039 (mp) REVERT: A 497 MET cc_start: 0.8031 (tmt) cc_final: 0.6954 (tmt) REVERT: A 598 MET cc_start: 0.8589 (tpp) cc_final: 0.7934 (tpt) REVERT: B 189 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8145 (tt) REVERT: B 284 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7539 (mtpp) REVERT: B 482 ASP cc_start: 0.8130 (t0) cc_final: 0.7845 (m-30) REVERT: B 497 MET cc_start: 0.8060 (tmt) cc_final: 0.7110 (tmt) REVERT: B 583 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8582 (t) REVERT: C 497 MET cc_start: 0.7960 (tmt) cc_final: 0.6747 (tmt) REVERT: C 583 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8518 (t) outliers start: 19 outliers final: 13 residues processed: 174 average time/residue: 1.8119 time to fit residues: 356.4637 Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.154574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121049 restraints weight = 36411.617| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.27 r_work: 0.2879 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12672 Z= 0.189 Angle : 0.456 4.433 17241 Z= 0.241 Chirality : 0.035 0.110 1989 Planarity : 0.004 0.052 2091 Dihedral : 8.120 139.196 1854 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 17.31 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.21), residues: 1593 helix: 2.40 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 178 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE C 413 TYR 0.005 0.001 TYR C 119 ARG 0.001 0.000 ARG C 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7223.20 seconds wall clock time: 126 minutes 5.95 seconds (7565.95 seconds total)