Starting phenix.real_space_refine on Fri Apr 12 08:03:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/04_2024/8tz3_41732_trim_updated.pdb" } resolution = 2.31 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= 0.004 sd= 0.153 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8412 2.51 5 N 1926 2.21 5 O 2202 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 481": "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-5288/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7934 SG CYS A 608 49.354 32.824 38.169 1.00 20.21 S ATOM 16063 SG CYS C 608 87.685 68.096 38.146 1.00 20.07 S ATOM 24192 SG CYS B 608 37.946 83.694 38.152 1.00 20.18 S Time building chain proxies: 11.23, per 1000 atoms: 0.45 Number of scatterers: 24810 At special positions: 0 Unit cell: (129.6, 127.44, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 6 11.00 O 2202 8.00 N 1926 7.00 C 8412 6.00 H 12165 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: 20.21 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 81 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.619A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 158 through 197 Proline residue: A 167 - end of helix removed outlier: 5.006A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 253 through 280 removed outlier: 3.686A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.659A pdb=" N LYS A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 347 through 360 Proline residue: A 351 - end of helix removed outlier: 4.542A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.598A pdb=" N GLY A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 4.725A pdb=" N GLY A 383 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 removed outlier: 3.917A 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 424 through 428 Processing helix chain 'A' and resid 438 through 481 removed outlier: 3.713A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.675A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 507 through 522 removed outlier: 3.920A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.551A pdb=" N LEU A 575 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 579 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 580 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 584 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.525A pdb=" N LYS A 590 " --> pdb=" O PRO A 587 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 593 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 618 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.619A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 158 through 197 Proline residue: C 167 - end of helix removed outlier: 5.006A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 No H-bonds generated for 'chain 'C' and resid 199 through 202' Processing helix chain 'C' and resid 204 through 222 Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 253 through 280 removed outlier: 3.687A pdb=" N GLY C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 314 through 329 removed outlier: 3.658A pdb=" N LYS C 320 " --> pdb=" O TRP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.557A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.599A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 388 removed outlier: 4.724A pdb=" N GLY C 383 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 removed outlier: 3.917A 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 424 through 428 Processing helix chain 'C' and resid 438 through 481 removed outlier: 3.712A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.675A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 507 through 522 removed outlier: 3.920A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 541 Processing helix chain 'C' and resid 556 through 565 Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.551A pdb=" N LEU C 575 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 576 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 577 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 579 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 580 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 584 " --> pdb=" O GLY C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 3.526A pdb=" N LYS C 590 " --> pdb=" O PRO C 587 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 593 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 removed outlier: 3.619A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 158 through 197 Proline residue: B 167 - end of helix removed outlier: 5.006A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'B' and resid 253 through 280 removed outlier: 3.686A pdb=" N GLY B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.659A pdb=" N LYS B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 351 through 360 removed outlier: 3.558A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.599A pdb=" N GLY B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.725A pdb=" N GLY B 383 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 removed outlier: 3.916A 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 424 through 428 Processing helix chain 'B' and resid 438 through 481 removed outlier: 3.713A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.675A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 507 through 522 removed outlier: 3.920A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.551A pdb=" N LEU B 575 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 579 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 580 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 584 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.525A pdb=" N LYS B 590 " --> pdb=" O PRO B 587 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 593 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 822 hydrogen bonds defined for protein. 2352 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: 9.62 Time building geometry restraints manager: 20.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 12147 1.02 - 1.22: 42 1.22 - 1.42: 5401 1.42 - 1.61: 7343 1.61 - 1.81: 180 Bond restraints: 25113 Sorted by residual: bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O4 LBN A 805 " pdb=" P1 LBN A 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O4 LBN C 805 " pdb=" P1 LBN C 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 25108 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.90: 271 105.90 - 112.97: 28614 112.97 - 120.04: 7432 120.04 - 127.10: 8593 127.10 - 134.17: 159 Bond angle restraints: 45069 Sorted by residual: angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 110.14 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " pdb=" O2 LBN C 806 " ideal model delta sigma weight residual 93.45 110.10 -16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O1 LBN A 806 " pdb=" P1 LBN A 806 " pdb=" O2 LBN A 806 " ideal model delta sigma weight residual 93.45 110.06 -16.61 3.00e+00 1.11e-01 3.07e+01 ... (remaining 45064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 11584 35.64 - 71.29: 431 71.29 - 106.93: 18 106.93 - 142.57: 3 142.57 - 178.21: 6 Dihedral angle restraints: 12042 sinusoidal: 6312 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 803 " pdb=" C2 LBN A 803 " pdb=" C3 LBN A 803 " pdb=" O7 LBN A 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.12 -178.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN B 803 " pdb=" C2 LBN B 803 " pdb=" C3 LBN B 803 " pdb=" O7 LBN B 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.14 -178.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 803 " pdb=" C2 LBN C 803 " pdb=" C3 LBN C 803 " pdb=" O7 LBN C 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.15 -178.18 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1183 0.039 - 0.078: 636 0.078 - 0.117: 147 0.117 - 0.156: 26 0.156 - 0.195: 3 Chirality restraints: 1995 Sorted by residual: chirality pdb=" C2 LBN A 805 " pdb=" C1 LBN A 805 " pdb=" C3 LBN A 805 " pdb=" O7 LBN A 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" C2 LBN C 805 " pdb=" C1 LBN C 805 " pdb=" C3 LBN C 805 " pdb=" O7 LBN C 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C2 LBN B 805 " pdb=" C1 LBN B 805 " pdb=" C3 LBN B 805 " pdb=" O7 LBN B 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1992 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO A 296 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO C 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO B 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.035 5.00e-02 4.00e+02 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 716 2.14 - 2.76: 44375 2.76 - 3.37: 68617 3.37 - 3.99: 90753 3.99 - 4.60: 143443 Nonbonded interactions: 347904 Sorted by model distance: nonbonded pdb=" O PHE C 223 " pdb="HH22 ARG C 599 " model vdw 1.530 1.850 nonbonded pdb=" O PHE B 223 " pdb="HH22 ARG B 599 " model vdw 1.532 1.850 nonbonded pdb=" O PHE A 223 " pdb="HH22 ARG A 599 " model vdw 1.532 1.850 nonbonded pdb=" O VAL C 298 " pdb=" HG SER C 302 " model vdw 1.540 1.850 nonbonded pdb=" O VAL B 298 " pdb=" HG SER B 302 " model vdw 1.564 1.850 ... (remaining 347899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 0.900 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: 0.290 Extract box with map and model: 4.830 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 82.650 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 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:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.149 12948 Z= 0.697 Angle : 0.991 16.712 17547 Z= 0.438 Chirality : 0.048 0.195 1995 Planarity : 0.006 0.062 2115 Dihedral : 16.560 178.214 4548 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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: -3.08 (0.17), residues: 1593 helix: -1.96 (0.11), residues: 1323 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.004 0.001 HIS B 367 PHE 0.022 0.002 PHE C 279 TYR 0.012 0.002 TYR A 285 ARG 0.002 0.001 ARG B 355 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.7105 (mtp) cc_final: 0.6829 (mtp) REVERT: A 228 THR cc_start: 0.8253 (p) cc_final: 0.8035 (p) REVERT: A 248 LEU cc_start: 0.8141 (tp) cc_final: 0.7831 (mp) REVERT: A 421 LYS cc_start: 0.7891 (mttt) cc_final: 0.7514 (mmtt) REVERT: A 483 TYR cc_start: 0.8200 (t80) cc_final: 0.7737 (t80) REVERT: A 508 GLN cc_start: 0.7509 (mt0) cc_final: 0.7051 (mp10) REVERT: A 590 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (ttmt) REVERT: C 129 MET cc_start: 0.6650 (mtp) cc_final: 0.6326 (mtp) REVERT: C 231 TYR cc_start: 0.7955 (t80) cc_final: 0.7543 (t80) REVERT: C 248 LEU cc_start: 0.7823 (tp) cc_final: 0.7592 (mp) REVERT: C 317 ILE cc_start: 0.8435 (mt) cc_final: 0.8159 (tp) REVERT: C 325 MET cc_start: 0.8319 (mtm) cc_final: 0.8106 (mtm) REVERT: C 355 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7341 (ttp80) REVERT: C 370 MET cc_start: 0.8699 (mtm) cc_final: 0.8373 (mtm) REVERT: C 421 LYS cc_start: 0.7873 (mttt) cc_final: 0.7668 (mmtp) REVERT: B 129 MET cc_start: 0.6740 (mtp) cc_final: 0.6533 (mtp) REVERT: B 151 ASP cc_start: 0.7696 (m-30) cc_final: 0.7422 (m-30) REVERT: B 231 TYR cc_start: 0.8021 (t80) cc_final: 0.7588 (t80) REVERT: B 248 LEU cc_start: 0.7926 (tp) cc_final: 0.7718 (mp) REVERT: B 325 MET cc_start: 0.8169 (mtm) cc_final: 0.7925 (mtm) REVERT: B 421 LYS cc_start: 0.7846 (mttt) cc_final: 0.7392 (mmtt) REVERT: B 440 GLU cc_start: 0.8230 (tt0) cc_final: 0.7934 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 2.1038 time to fit residues: 537.9868 Evaluate side-chains 183 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN C 426 ASN B 423 ASN B 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12948 Z= 0.160 Angle : 0.491 4.794 17547 Z= 0.263 Chirality : 0.036 0.121 1995 Planarity : 0.004 0.047 2115 Dihedral : 14.780 147.945 1998 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.40 % Allowed : 7.76 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1593 helix: 0.85 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 323 HIS 0.003 0.001 HIS C 288 PHE 0.017 0.001 PHE B 279 TYR 0.010 0.001 TYR B 519 ARG 0.002 0.000 ARG A 599 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 2.248 Fit side-chains REVERT: A 129 MET cc_start: 0.7007 (mtp) cc_final: 0.6758 (mtp) REVERT: A 193 LEU cc_start: 0.8221 (mt) cc_final: 0.7932 (mm) REVERT: A 204 GLN cc_start: 0.7813 (tt0) cc_final: 0.7558 (tt0) REVERT: A 248 LEU cc_start: 0.8007 (tp) cc_final: 0.7601 (mp) REVERT: A 317 ILE cc_start: 0.8464 (mt) cc_final: 0.8218 (tp) REVERT: A 483 TYR cc_start: 0.8177 (t80) cc_final: 0.7694 (t80) REVERT: A 497 MET cc_start: 0.8272 (tmt) cc_final: 0.7890 (tmm) REVERT: A 508 GLN cc_start: 0.7527 (mt0) cc_final: 0.7075 (mp10) REVERT: A 590 LYS cc_start: 0.8240 (tttt) cc_final: 0.7985 (ttmt) REVERT: C 129 MET cc_start: 0.6771 (mtp) cc_final: 0.6447 (mtp) REVERT: C 231 TYR cc_start: 0.7877 (t80) cc_final: 0.7417 (t80) REVERT: C 317 ILE cc_start: 0.8457 (mt) cc_final: 0.8107 (tp) REVERT: C 325 MET cc_start: 0.8519 (mtm) cc_final: 0.7967 (mtm) REVERT: C 355 ARG cc_start: 0.7669 (ttt180) cc_final: 0.7304 (ttp80) REVERT: C 370 MET cc_start: 0.8533 (mtm) cc_final: 0.8233 (mtm) REVERT: C 421 LYS cc_start: 0.7888 (mttt) cc_final: 0.7655 (mmtp) REVERT: B 142 VAL cc_start: 0.7536 (t) cc_final: 0.7146 (p) REVERT: B 231 TYR cc_start: 0.7922 (t80) cc_final: 0.7514 (t80) REVERT: B 248 LEU cc_start: 0.7942 (tp) cc_final: 0.7615 (mp) REVERT: B 325 MET cc_start: 0.8510 (mtm) cc_final: 0.7832 (mtm) REVERT: B 421 LYS cc_start: 0.7837 (mttt) cc_final: 0.7382 (mmtt) REVERT: B 440 GLU cc_start: 0.7935 (tt0) cc_final: 0.7618 (tt0) outliers start: 5 outliers final: 0 residues processed: 188 average time/residue: 1.9771 time to fit residues: 426.5494 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 204 GLN B 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12948 Z= 0.223 Angle : 0.525 5.875 17547 Z= 0.280 Chirality : 0.038 0.121 1995 Planarity : 0.004 0.047 2115 Dihedral : 13.943 146.455 1998 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.71 % Allowed : 8.16 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1593 helix: 1.48 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.33 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.026 0.002 PHE A 279 TYR 0.009 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 1.956 Fit side-chains REVERT: A 193 LEU cc_start: 0.8236 (mt) cc_final: 0.7958 (mm) REVERT: A 248 LEU cc_start: 0.8181 (tp) cc_final: 0.7733 (mp) REVERT: A 317 ILE cc_start: 0.8548 (mt) cc_final: 0.8280 (tp) REVERT: A 483 TYR cc_start: 0.8169 (t80) cc_final: 0.7688 (t80) REVERT: A 590 LYS cc_start: 0.8197 (tttt) cc_final: 0.7996 (ttmt) REVERT: C 129 MET cc_start: 0.6682 (mtp) cc_final: 0.6392 (mtp) REVERT: C 231 TYR cc_start: 0.8105 (t80) cc_final: 0.7701 (t80) REVERT: C 355 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7293 (ttp80) REVERT: C 370 MET cc_start: 0.8617 (mtm) cc_final: 0.8285 (mtm) REVERT: B 142 VAL cc_start: 0.7569 (t) cc_final: 0.7174 (p) REVERT: B 231 TYR cc_start: 0.7932 (t80) cc_final: 0.7515 (t80) REVERT: B 248 LEU cc_start: 0.8105 (tp) cc_final: 0.7719 (mp) REVERT: B 305 MET cc_start: 0.8302 (mmm) cc_final: 0.8071 (mmm) REVERT: B 325 MET cc_start: 0.8532 (mtm) cc_final: 0.7869 (mtm) REVERT: B 421 LYS cc_start: 0.7895 (mttt) cc_final: 0.7393 (mmtt) REVERT: B 440 GLU cc_start: 0.8054 (tt0) cc_final: 0.7789 (tt0) REVERT: B 448 SER cc_start: 0.8794 (m) cc_final: 0.8588 (p) outliers start: 9 outliers final: 5 residues processed: 182 average time/residue: 1.9222 time to fit residues: 395.4050 Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 204 GLN B 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12948 Z= 0.182 Angle : 0.481 5.187 17547 Z= 0.255 Chirality : 0.036 0.121 1995 Planarity : 0.004 0.043 2115 Dihedral : 13.277 145.407 1998 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 8.31 % Favored : 90.97 % 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: 2.23 (0.21), residues: 1593 helix: 1.83 (0.15), residues: 1317 sheet: None (None), residues: 0 loop : -0.10 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.021 0.002 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.003 0.000 ARG B 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 1.836 Fit side-chains REVERT: A 193 LEU cc_start: 0.8237 (mt) cc_final: 0.7960 (mm) REVERT: A 248 LEU cc_start: 0.8165 (tp) cc_final: 0.7694 (mp) REVERT: A 317 ILE cc_start: 0.8550 (mt) cc_final: 0.8273 (tp) REVERT: A 483 TYR cc_start: 0.8129 (t80) cc_final: 0.7646 (t80) REVERT: A 497 MET cc_start: 0.8351 (tmt) cc_final: 0.7997 (tmm) REVERT: A 554 MET cc_start: 0.8575 (ptt) cc_final: 0.8308 (ptt) REVERT: C 129 MET cc_start: 0.6640 (mtp) cc_final: 0.6432 (mtp) REVERT: C 231 TYR cc_start: 0.8070 (t80) cc_final: 0.7594 (t80) REVERT: C 317 ILE cc_start: 0.8479 (mt) cc_final: 0.8109 (tp) REVERT: C 355 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7418 (ttp80) REVERT: C 472 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8287 (t) REVERT: B 142 VAL cc_start: 0.7582 (t) cc_final: 0.7186 (p) REVERT: B 231 TYR cc_start: 0.7923 (t80) cc_final: 0.7430 (t80) REVERT: B 248 LEU cc_start: 0.8122 (tp) cc_final: 0.7708 (mp) REVERT: B 305 MET cc_start: 0.8300 (mmm) cc_final: 0.8064 (mmm) REVERT: B 325 MET cc_start: 0.8614 (mtm) cc_final: 0.7869 (mtm) REVERT: B 421 LYS cc_start: 0.7868 (mttt) cc_final: 0.7381 (mmtt) REVERT: B 440 GLU cc_start: 0.8038 (tt0) cc_final: 0.7759 (tt0) REVERT: B 448 SER cc_start: 0.8779 (m) cc_final: 0.8553 (p) outliers start: 9 outliers final: 2 residues processed: 177 average time/residue: 1.9875 time to fit residues: 395.5164 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 204 GLN B 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12948 Z= 0.318 Angle : 0.623 7.278 17547 Z= 0.330 Chirality : 0.041 0.142 1995 Planarity : 0.005 0.045 2115 Dihedral : 14.345 148.154 1998 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.19 % Allowed : 8.31 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.21), residues: 1593 helix: 1.49 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 323 HIS 0.006 0.001 HIS C 288 PHE 0.033 0.003 PHE A 279 TYR 0.013 0.002 TYR C 310 ARG 0.007 0.001 ARG B 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.059 Fit side-chains REVERT: A 193 LEU cc_start: 0.8242 (mt) cc_final: 0.7975 (mm) REVERT: A 231 TYR cc_start: 0.8050 (t80) cc_final: 0.7636 (t80) REVERT: A 248 LEU cc_start: 0.8317 (tp) cc_final: 0.7850 (mp) REVERT: A 317 ILE cc_start: 0.8440 (mt) cc_final: 0.8164 (tp) REVERT: A 355 ARG cc_start: 0.7540 (ttt-90) cc_final: 0.7294 (ttt180) REVERT: A 483 TYR cc_start: 0.8143 (t80) cc_final: 0.7624 (t80) REVERT: C 129 MET cc_start: 0.6710 (mtp) cc_final: 0.6502 (mtp) REVERT: C 231 TYR cc_start: 0.8192 (t80) cc_final: 0.7762 (t80) REVERT: C 355 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7445 (ttp80) REVERT: B 142 VAL cc_start: 0.7529 (t) cc_final: 0.7163 (p) REVERT: B 231 TYR cc_start: 0.7982 (t80) cc_final: 0.7523 (t80) REVERT: B 248 LEU cc_start: 0.8246 (tp) cc_final: 0.7848 (mp) REVERT: B 305 MET cc_start: 0.8309 (mmm) cc_final: 0.8022 (mmm) REVERT: B 325 MET cc_start: 0.8630 (mtm) cc_final: 0.7955 (mtm) REVERT: B 421 LYS cc_start: 0.7873 (mttt) cc_final: 0.7372 (mmtp) REVERT: B 440 GLU cc_start: 0.8072 (tt0) cc_final: 0.7796 (tt0) REVERT: B 448 SER cc_start: 0.8791 (m) cc_final: 0.8569 (p) outliers start: 15 outliers final: 10 residues processed: 179 average time/residue: 1.9319 time to fit residues: 389.8913 Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 426 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12948 Z= 0.251 Angle : 0.548 6.343 17547 Z= 0.291 Chirality : 0.039 0.122 1995 Planarity : 0.004 0.044 2115 Dihedral : 14.127 151.492 1998 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.03 % Allowed : 8.55 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.21), residues: 1593 helix: 1.61 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -0.09 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.027 0.002 PHE A 279 TYR 0.011 0.002 TYR C 310 ARG 0.004 0.001 ARG C 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 2.000 Fit side-chains REVERT: A 193 LEU cc_start: 0.8184 (mt) cc_final: 0.7919 (mm) REVERT: A 231 TYR cc_start: 0.7990 (t80) cc_final: 0.7585 (t80) REVERT: A 248 LEU cc_start: 0.8261 (tp) cc_final: 0.7796 (mp) REVERT: A 317 ILE cc_start: 0.8451 (mt) cc_final: 0.8169 (tp) REVERT: A 483 TYR cc_start: 0.8149 (t80) cc_final: 0.7660 (t80) REVERT: C 129 MET cc_start: 0.6765 (mtp) cc_final: 0.6558 (mtp) REVERT: C 355 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7430 (ttp80) REVERT: B 142 VAL cc_start: 0.7537 (t) cc_final: 0.7180 (p) REVERT: B 231 TYR cc_start: 0.7976 (t80) cc_final: 0.7555 (t80) REVERT: B 248 LEU cc_start: 0.8238 (tp) cc_final: 0.7820 (mp) REVERT: B 305 MET cc_start: 0.8305 (mmm) cc_final: 0.8020 (mmm) REVERT: B 325 MET cc_start: 0.8623 (mtm) cc_final: 0.7820 (mtm) REVERT: B 421 LYS cc_start: 0.7867 (mttt) cc_final: 0.7372 (mmtp) REVERT: B 440 GLU cc_start: 0.8087 (tt0) cc_final: 0.7818 (tt0) REVERT: B 448 SER cc_start: 0.8775 (m) cc_final: 0.8532 (p) outliers start: 13 outliers final: 10 residues processed: 175 average time/residue: 1.9666 time to fit residues: 389.6744 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12948 Z= 0.141 Angle : 0.446 5.436 17547 Z= 0.235 Chirality : 0.035 0.121 1995 Planarity : 0.003 0.040 2115 Dihedral : 12.918 149.650 1998 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.79 % Allowed : 8.87 % Favored : 90.34 % 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: 2.57 (0.21), residues: 1593 helix: 2.06 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -0.02 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.003 0.001 HIS C 288 PHE 0.019 0.001 PHE C 279 TYR 0.007 0.001 TYR C 310 ARG 0.002 0.000 ARG A 557 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8176 (mt) cc_final: 0.7904 (mm) REVERT: A 248 LEU cc_start: 0.8132 (tp) cc_final: 0.7677 (mp) REVERT: A 317 ILE cc_start: 0.8557 (mt) cc_final: 0.8274 (tp) REVERT: A 483 TYR cc_start: 0.8130 (t80) cc_final: 0.7646 (t80) REVERT: A 497 MET cc_start: 0.8369 (tmt) cc_final: 0.7855 (tmm) REVERT: C 129 MET cc_start: 0.6739 (mtp) cc_final: 0.6526 (mtp) REVERT: C 231 TYR cc_start: 0.8053 (t80) cc_final: 0.7660 (t80) REVERT: C 317 ILE cc_start: 0.8468 (mt) cc_final: 0.8086 (tp) REVERT: C 355 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7336 (ttp80) REVERT: C 472 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8276 (t) REVERT: C 577 ILE cc_start: 0.8356 (pt) cc_final: 0.8099 (pp) REVERT: B 142 VAL cc_start: 0.7569 (t) cc_final: 0.7228 (p) REVERT: B 231 TYR cc_start: 0.7893 (t80) cc_final: 0.7476 (t80) REVERT: B 248 LEU cc_start: 0.8057 (tp) cc_final: 0.7654 (mp) REVERT: B 305 MET cc_start: 0.8271 (mmm) cc_final: 0.8062 (mmm) REVERT: B 325 MET cc_start: 0.8633 (mtm) cc_final: 0.7872 (mtm) REVERT: B 421 LYS cc_start: 0.7803 (mttt) cc_final: 0.7380 (mmtt) REVERT: B 440 GLU cc_start: 0.7984 (tt0) cc_final: 0.7702 (tt0) REVERT: B 448 SER cc_start: 0.8777 (m) cc_final: 0.8529 (p) outliers start: 10 outliers final: 0 residues processed: 175 average time/residue: 1.9210 time to fit residues: 379.4318 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 472 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 146 optimal weight: 2.9990 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12948 Z= 0.188 Angle : 0.496 6.183 17547 Z= 0.262 Chirality : 0.037 0.125 1995 Planarity : 0.004 0.042 2115 Dihedral : 13.466 150.050 1998 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.63 % Allowed : 9.42 % Favored : 89.94 % 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: 2.50 (0.21), residues: 1593 helix: 2.00 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : 0.02 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.004 0.001 HIS B 288 PHE 0.022 0.002 PHE A 279 TYR 0.008 0.001 TYR C 310 ARG 0.003 0.000 ARG C 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8150 (mt) cc_final: 0.7887 (mm) REVERT: A 231 TYR cc_start: 0.7953 (t80) cc_final: 0.7516 (t80) REVERT: A 248 LEU cc_start: 0.8189 (tp) cc_final: 0.7731 (mp) REVERT: A 317 ILE cc_start: 0.8550 (mt) cc_final: 0.8260 (tp) REVERT: A 483 TYR cc_start: 0.8122 (t80) cc_final: 0.7632 (t80) REVERT: A 497 MET cc_start: 0.8408 (tmt) cc_final: 0.7732 (tmm) REVERT: C 129 MET cc_start: 0.6752 (mtp) cc_final: 0.6538 (mtp) REVERT: C 231 TYR cc_start: 0.8125 (t80) cc_final: 0.7662 (t80) REVERT: C 355 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7433 (ttp80) REVERT: C 577 ILE cc_start: 0.8365 (pt) cc_final: 0.8101 (pp) REVERT: B 142 VAL cc_start: 0.7566 (t) cc_final: 0.7221 (p) REVERT: B 231 TYR cc_start: 0.7929 (t80) cc_final: 0.7533 (t80) REVERT: B 248 LEU cc_start: 0.8095 (tp) cc_final: 0.7694 (mp) REVERT: B 305 MET cc_start: 0.8288 (mmm) cc_final: 0.8061 (mmm) REVERT: B 325 MET cc_start: 0.8655 (mtm) cc_final: 0.7757 (mtm) REVERT: B 421 LYS cc_start: 0.7824 (mttt) cc_final: 0.7396 (mmtt) REVERT: B 440 GLU cc_start: 0.8029 (tt0) cc_final: 0.7750 (tt0) REVERT: B 448 SER cc_start: 0.8777 (m) cc_final: 0.8554 (p) outliers start: 8 outliers final: 7 residues processed: 174 average time/residue: 1.9420 time to fit residues: 381.2466 Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12948 Z= 0.172 Angle : 0.478 6.054 17547 Z= 0.251 Chirality : 0.036 0.122 1995 Planarity : 0.004 0.041 2115 Dihedral : 13.360 151.103 1998 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.87 % 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: 2.56 (0.21), residues: 1593 helix: 2.04 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.022 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.003 0.000 ARG C 589 *********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8127 (mt) cc_final: 0.7866 (mm) REVERT: A 248 LEU cc_start: 0.8173 (tp) cc_final: 0.7714 (mp) REVERT: A 317 ILE cc_start: 0.8543 (mt) cc_final: 0.8267 (tp) REVERT: A 483 TYR cc_start: 0.8150 (t80) cc_final: 0.7675 (t80) REVERT: A 497 MET cc_start: 0.8392 (tmt) cc_final: 0.7814 (tmm) REVERT: C 129 MET cc_start: 0.6745 (mtp) cc_final: 0.6529 (mtp) REVERT: C 231 TYR cc_start: 0.8104 (t80) cc_final: 0.7630 (t80) REVERT: C 317 ILE cc_start: 0.8451 (mt) cc_final: 0.8061 (tp) REVERT: C 355 ARG cc_start: 0.7767 (ttt180) cc_final: 0.7427 (ttp80) REVERT: C 472 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8280 (t) REVERT: C 556 MET cc_start: 0.7700 (mtp) cc_final: 0.7484 (mtp) REVERT: C 577 ILE cc_start: 0.8354 (pt) cc_final: 0.8092 (pp) REVERT: B 142 VAL cc_start: 0.7565 (t) cc_final: 0.7222 (p) REVERT: B 231 TYR cc_start: 0.7913 (t80) cc_final: 0.7525 (t80) REVERT: B 248 LEU cc_start: 0.8071 (tp) cc_final: 0.7677 (mp) REVERT: B 325 MET cc_start: 0.8656 (mtm) cc_final: 0.7748 (mtm) REVERT: B 421 LYS cc_start: 0.7824 (mttt) cc_final: 0.7394 (mmtt) REVERT: B 440 GLU cc_start: 0.8018 (tt0) cc_final: 0.7741 (tt0) REVERT: B 448 SER cc_start: 0.8764 (m) cc_final: 0.8522 (p) outliers start: 6 outliers final: 4 residues processed: 171 average time/residue: 2.0037 time to fit residues: 386.7298 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12948 Z= 0.156 Angle : 0.465 6.853 17547 Z= 0.244 Chirality : 0.036 0.124 1995 Planarity : 0.003 0.041 2115 Dihedral : 13.109 150.851 1998 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.87 % 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: 2.71 (0.21), residues: 1593 helix: 2.14 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : 0.20 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.004 0.001 HIS B 288 PHE 0.019 0.001 PHE C 279 TYR 0.007 0.001 TYR C 310 ARG 0.002 0.000 ARG C 589 ********************** 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 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 TYR 109 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 LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8129 (mt) cc_final: 0.7868 (mm) REVERT: A 248 LEU cc_start: 0.8131 (tp) cc_final: 0.7672 (mp) REVERT: A 317 ILE cc_start: 0.8538 (mt) cc_final: 0.8275 (tp) REVERT: A 483 TYR cc_start: 0.8155 (t80) cc_final: 0.7674 (t80) REVERT: A 497 MET cc_start: 0.8390 (tmt) cc_final: 0.7816 (tmm) REVERT: C 129 MET cc_start: 0.6745 (mtp) cc_final: 0.6530 (mtp) REVERT: C 231 TYR cc_start: 0.8095 (t80) cc_final: 0.7625 (t80) REVERT: C 317 ILE cc_start: 0.8477 (mt) cc_final: 0.8091 (tp) REVERT: C 355 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7349 (ttp80) REVERT: C 472 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (t) REVERT: C 556 MET cc_start: 0.7705 (mtp) cc_final: 0.7500 (mtp) REVERT: C 577 ILE cc_start: 0.8349 (pt) cc_final: 0.8086 (pp) REVERT: B 142 VAL cc_start: 0.7567 (t) cc_final: 0.7225 (p) REVERT: B 231 TYR cc_start: 0.7894 (t80) cc_final: 0.7510 (t80) REVERT: B 248 LEU cc_start: 0.8053 (tp) cc_final: 0.7655 (mp) REVERT: B 325 MET cc_start: 0.8640 (mtm) cc_final: 0.7819 (mtm) REVERT: B 421 LYS cc_start: 0.7840 (mttt) cc_final: 0.7373 (mmtp) REVERT: B 440 GLU cc_start: 0.7993 (tt0) cc_final: 0.7719 (tt0) REVERT: B 448 SER cc_start: 0.8764 (m) cc_final: 0.8516 (p) outliers start: 6 outliers final: 4 residues processed: 171 average time/residue: 1.9535 time to fit residues: 376.4434 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109226 restraints weight = 29170.871| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.03 r_work: 0.3051 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12948 Z= 0.162 Angle : 0.471 6.307 17547 Z= 0.247 Chirality : 0.036 0.121 1995 Planarity : 0.003 0.041 2115 Dihedral : 13.110 150.852 1998 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.79 % 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: 2.71 (0.21), residues: 1593 helix: 2.14 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : 0.20 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.020 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG C 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8031.82 seconds wall clock time: 143 minutes 19.32 seconds (8599.32 seconds total)