Starting phenix.real_space_refine on Sat Feb 17 23:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhi_29086/02_2024/8fhi_29086_neut_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 144 5.16 5 C 13044 2.51 5 N 3332 2.21 5 O 3580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "D ASP 71": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20116 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4883 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4883 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Chain: "C" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4883 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Chain: "D" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4883 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'3VV': 1, 'ERG': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'POV:plan-1': 1, '3VV:plan-6': 1, '3VV:plan-5': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'3VV': 1, 'ERG': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'POV:plan-1': 1, '3VV:plan-6': 1, '3VV:plan-5': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'3VV': 1, 'ERG': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'POV:plan-1': 1, '3VV:plan-6': 1, '3VV:plan-5': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'3VV': 1, 'ERG': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'POV:plan-1': 1, '3VV:plan-6': 1, '3VV:plan-5': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 10.18, per 1000 atoms: 0.51 Number of scatterers: 20116 At special positions: 0 Unit cell: (138.61, 138.61, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 16 15.00 O 3580 8.00 N 3332 7.00 C 13044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.50 Conformation dependent library (CDL) restraints added in 3.2 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 59.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.459A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.528A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.794A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 380 through 409 Proline residue: A 405 - end of helix removed outlier: 3.815A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 424 through 444 Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.513A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 486 Proline residue: A 477 - end of helix removed outlier: 4.007A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 511 removed outlier: 5.023A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.654A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 607 removed outlier: 3.924A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.459A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.527A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.794A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 380 through 409 Proline residue: B 405 - end of helix removed outlier: 3.815A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 424 through 444 Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.513A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 486 Proline residue: B 477 - end of helix removed outlier: 4.008A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 511 removed outlier: 5.023A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 removed outlier: 3.654A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 607 removed outlier: 3.924A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.459A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.528A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.795A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 380 through 409 Proline residue: C 405 - end of helix removed outlier: 3.815A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 424 through 444 Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.514A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 Proline residue: C 477 - end of helix removed outlier: 4.007A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 511 removed outlier: 5.023A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 removed outlier: 3.655A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 607 removed outlier: 3.923A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 210 through 221 removed outlier: 4.459A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 261 Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.528A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.794A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 380 through 409 Proline residue: D 405 - end of helix removed outlier: 3.815A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 424 through 444 Processing helix chain 'D' and resid 450 through 471 removed outlier: 3.514A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 Proline residue: D 477 - end of helix removed outlier: 4.007A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 511 removed outlier: 5.023A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 523 No H-bonds generated for 'chain 'D' and resid 521 through 523' Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 removed outlier: 3.654A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 607 removed outlier: 3.923A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 6.243A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 636 removed outlier: 6.243A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 636 removed outlier: 6.243A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 636 removed outlier: 6.242A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 912 hydrogen bonds defined for protein. 2688 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: 6.47 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3172 1.32 - 1.44: 5510 1.44 - 1.56: 11642 1.56 - 1.69: 36 1.69 - 1.81: 232 Bond restraints: 20592 Sorted by residual: bond pdb=" C49 3VV D 804 " pdb=" C50 3VV D 804 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C49 3VV C 803 " pdb=" C50 3VV C 803 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C49 3VV A 803 " pdb=" C50 3VV A 803 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C49 3VV B 803 " pdb=" C50 3VV B 803 " ideal model delta sigma weight residual 1.291 1.520 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C49 3VV C 803 " pdb=" O48 3VV C 803 " ideal model delta sigma weight residual 1.621 1.406 0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 20587 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.83: 409 104.83 - 112.16: 10187 112.16 - 119.48: 7455 119.48 - 126.80: 9660 126.80 - 134.13: 305 Bond angle restraints: 28016 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N GLN A 68 " pdb=" CA GLN A 68 " ideal model delta sigma weight residual 123.03 116.09 6.94 1.34e+00 5.57e-01 2.68e+01 angle pdb=" C ASN B 67 " pdb=" N GLN B 68 " pdb=" CA GLN B 68 " ideal model delta sigma weight residual 123.03 116.09 6.94 1.34e+00 5.57e-01 2.68e+01 angle pdb=" C ASN D 67 " pdb=" N GLN D 68 " pdb=" CA GLN D 68 " ideal model delta sigma weight residual 123.03 116.13 6.90 1.34e+00 5.57e-01 2.65e+01 angle pdb=" C ASN C 67 " pdb=" N GLN C 68 " pdb=" CA GLN C 68 " ideal model delta sigma weight residual 123.03 116.13 6.90 1.34e+00 5.57e-01 2.65e+01 angle pdb=" N63 3VV D 804 " pdb=" C62 3VV D 804 " pdb=" N64 3VV D 804 " ideal model delta sigma weight residual 103.64 118.78 -15.14 3.00e+00 1.11e-01 2.55e+01 ... (remaining 28011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 12352 30.61 - 61.22: 252 61.22 - 91.83: 32 91.83 - 122.44: 0 122.44 - 153.05: 4 Dihedral angle restraints: 12640 sinusoidal: 5512 harmonic: 7128 Sorted by residual: dihedral pdb=" C3 POV A 804 " pdb=" C31 POV A 804 " pdb=" O31 POV A 804 " pdb=" C32 POV A 804 " ideal model delta sinusoidal sigma weight residual 172.61 -34.34 -153.05 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 POV D 801 " pdb=" C31 POV D 801 " pdb=" O31 POV D 801 " pdb=" C32 POV D 801 " ideal model delta sinusoidal sigma weight residual 172.61 -34.35 -153.04 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 POV C 804 " pdb=" C31 POV C 804 " pdb=" O31 POV C 804 " pdb=" C32 POV C 804 " ideal model delta sinusoidal sigma weight residual 172.61 -34.45 -152.94 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 12637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2329 0.044 - 0.089: 688 0.089 - 0.133: 123 0.133 - 0.177: 28 0.177 - 0.222: 12 Chirality restraints: 3180 Sorted by residual: chirality pdb=" C31 3VV A 803 " pdb=" C29 3VV A 803 " pdb=" C33 3VV A 803 " pdb=" O32 3VV A 803 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C31 3VV C 803 " pdb=" C29 3VV C 803 " pdb=" C33 3VV C 803 " pdb=" O32 3VV C 803 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C31 3VV B 803 " pdb=" C29 3VV B 803 " pdb=" C33 3VV B 803 " pdb=" O32 3VV B 803 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3177 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 3VV D 804 " -0.250 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" C24 3VV D 804 " 0.052 2.00e-02 2.50e+03 pdb=" C26 3VV D 804 " 0.027 2.00e-02 2.50e+03 pdb=" N23 3VV D 804 " 0.358 2.00e-02 2.50e+03 pdb=" O25 3VV D 804 " -0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 3VV B 803 " 0.250 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" C24 3VV B 803 " -0.052 2.00e-02 2.50e+03 pdb=" C26 3VV B 803 " -0.028 2.00e-02 2.50e+03 pdb=" N23 3VV B 803 " -0.358 2.00e-02 2.50e+03 pdb=" O25 3VV B 803 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 3VV C 803 " -0.250 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" C24 3VV C 803 " 0.052 2.00e-02 2.50e+03 pdb=" C26 3VV C 803 " 0.028 2.00e-02 2.50e+03 pdb=" N23 3VV C 803 " 0.358 2.00e-02 2.50e+03 pdb=" O25 3VV C 803 " -0.187 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5655 2.81 - 3.34: 18762 3.34 - 3.86: 34387 3.86 - 4.38: 39988 4.38 - 4.90: 68983 Nonbonded interactions: 167775 Sorted by model distance: nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.293 2.440 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.293 2.440 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.293 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.294 2.440 nonbonded pdb=" OD2 ASP D 489 " pdb=" OG1 THR D 581 " model vdw 2.344 2.440 ... (remaining 167770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 638 or resid 802)) selection = (chain 'B' and (resid 28 through 638 or resid 802)) selection = (chain 'C' and (resid 28 through 638 or resid 802)) selection = (chain 'D' and (resid 28 through 638 or resid 802)) } 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: 1.180 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: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 53.400 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.009 0.229 20592 Z= 0.574 Angle : 0.851 15.137 28016 Z= 0.447 Chirality : 0.045 0.222 3180 Planarity : 0.011 0.214 3468 Dihedral : 13.432 153.048 8032 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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 (0.14), residues: 2424 helix: -1.07 (0.11), residues: 1496 sheet: -2.85 (0.39), residues: 124 loop : -1.74 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.003 0.001 HIS D 201 PHE 0.017 0.002 PHE C 537 TYR 0.010 0.001 TYR B 216 ARG 0.002 0.000 ARG C 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 2.237 Fit side-chains REVERT: A 42 GLU cc_start: 0.8313 (tp30) cc_final: 0.7957 (tp30) REVERT: A 43 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7357 (tpp80) REVERT: A 93 GLU cc_start: 0.8209 (mp0) cc_final: 0.7893 (pm20) REVERT: A 111 LEU cc_start: 0.8780 (mt) cc_final: 0.8477 (mt) REVERT: A 119 THR cc_start: 0.8604 (p) cc_final: 0.8285 (t) REVERT: A 130 LEU cc_start: 0.8557 (tp) cc_final: 0.8237 (tp) REVERT: A 218 LEU cc_start: 0.8552 (tp) cc_final: 0.8205 (tt) REVERT: A 222 TYR cc_start: 0.7068 (m-80) cc_final: 0.6761 (m-80) REVERT: A 262 LYS cc_start: 0.8360 (mmtp) cc_final: 0.8156 (mmtt) REVERT: A 300 LYS cc_start: 0.8613 (mttt) cc_final: 0.8411 (mmmt) REVERT: A 306 GLN cc_start: 0.8609 (mt0) cc_final: 0.8211 (mt0) REVERT: A 398 ILE cc_start: 0.9167 (mt) cc_final: 0.8886 (mt) REVERT: A 425 PHE cc_start: 0.8847 (m-80) cc_final: 0.8333 (m-80) REVERT: A 491 MET cc_start: 0.7925 (mmt) cc_final: 0.7680 (mmm) REVERT: B 42 GLU cc_start: 0.8325 (tp30) cc_final: 0.7951 (tp30) REVERT: B 43 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7365 (tpp80) REVERT: B 93 GLU cc_start: 0.8215 (mp0) cc_final: 0.7896 (pm20) REVERT: B 111 LEU cc_start: 0.8781 (mt) cc_final: 0.8485 (mt) REVERT: B 119 THR cc_start: 0.8594 (p) cc_final: 0.8264 (t) REVERT: B 130 LEU cc_start: 0.8566 (tp) cc_final: 0.8247 (tp) REVERT: B 218 LEU cc_start: 0.8554 (tp) cc_final: 0.8196 (tt) REVERT: B 222 TYR cc_start: 0.7076 (m-80) cc_final: 0.6771 (m-80) REVERT: B 262 LYS cc_start: 0.8366 (mmtp) cc_final: 0.8157 (mmtt) REVERT: B 300 LYS cc_start: 0.8616 (mttt) cc_final: 0.8410 (mmmt) REVERT: B 306 GLN cc_start: 0.8599 (mt0) cc_final: 0.8224 (mt0) REVERT: B 398 ILE cc_start: 0.9162 (mt) cc_final: 0.8878 (mt) REVERT: B 403 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 415 TYR cc_start: 0.8374 (t80) cc_final: 0.7467 (t80) REVERT: B 425 PHE cc_start: 0.8840 (m-80) cc_final: 0.8338 (m-80) REVERT: B 491 MET cc_start: 0.7926 (mmt) cc_final: 0.7673 (mmm) REVERT: C 42 GLU cc_start: 0.8319 (tp30) cc_final: 0.7950 (tp30) REVERT: C 43 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7367 (tpp80) REVERT: C 93 GLU cc_start: 0.8222 (mp0) cc_final: 0.7901 (pm20) REVERT: C 111 LEU cc_start: 0.8785 (mt) cc_final: 0.8480 (mt) REVERT: C 119 THR cc_start: 0.8591 (p) cc_final: 0.8259 (t) REVERT: C 130 LEU cc_start: 0.8572 (tp) cc_final: 0.8249 (tp) REVERT: C 218 LEU cc_start: 0.8556 (tp) cc_final: 0.8188 (tt) REVERT: C 222 TYR cc_start: 0.7077 (m-80) cc_final: 0.6777 (m-80) REVERT: C 262 LYS cc_start: 0.8373 (mmtp) cc_final: 0.8165 (mmtt) REVERT: C 300 LYS cc_start: 0.8616 (mttt) cc_final: 0.8413 (mmmt) REVERT: C 306 GLN cc_start: 0.8611 (mt0) cc_final: 0.8209 (mt0) REVERT: C 398 ILE cc_start: 0.9163 (mt) cc_final: 0.8881 (mt) REVERT: C 425 PHE cc_start: 0.8858 (m-80) cc_final: 0.8359 (m-80) REVERT: C 491 MET cc_start: 0.7925 (mmt) cc_final: 0.7674 (mmm) REVERT: D 42 GLU cc_start: 0.8319 (tp30) cc_final: 0.7954 (tp30) REVERT: D 43 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7367 (tpp80) REVERT: D 93 GLU cc_start: 0.8220 (mp0) cc_final: 0.7898 (pm20) REVERT: D 111 LEU cc_start: 0.8784 (mt) cc_final: 0.8478 (mt) REVERT: D 119 THR cc_start: 0.8591 (p) cc_final: 0.8258 (t) REVERT: D 130 LEU cc_start: 0.8563 (tp) cc_final: 0.8243 (tp) REVERT: D 218 LEU cc_start: 0.8551 (tp) cc_final: 0.8202 (tt) REVERT: D 222 TYR cc_start: 0.7076 (m-80) cc_final: 0.6769 (m-80) REVERT: D 262 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8161 (mmtt) REVERT: D 300 LYS cc_start: 0.8615 (mttt) cc_final: 0.8412 (mmmt) REVERT: D 306 GLN cc_start: 0.8611 (mt0) cc_final: 0.8211 (mt0) REVERT: D 398 ILE cc_start: 0.9165 (mt) cc_final: 0.8881 (mt) REVERT: D 425 PHE cc_start: 0.8845 (m-80) cc_final: 0.8341 (m-80) REVERT: D 491 MET cc_start: 0.7926 (mmt) cc_final: 0.7674 (mmm) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.3372 time to fit residues: 271.7425 Evaluate side-chains 319 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 185 HIS A 192 GLN A 206 GLN A 370 GLN A 509 HIS A 636 HIS B 51 GLN B 185 HIS B 192 GLN B 206 GLN B 370 GLN B 509 HIS B 636 HIS C 51 GLN C 185 HIS C 192 GLN C 206 GLN C 370 GLN C 509 HIS C 636 HIS D 51 GLN D 185 HIS D 192 GLN D 206 GLN D 370 GLN D 509 HIS D 636 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20592 Z= 0.167 Angle : 0.533 7.956 28016 Z= 0.257 Chirality : 0.038 0.182 3180 Planarity : 0.004 0.046 3468 Dihedral : 10.385 101.036 3412 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.66 % Allowed : 8.71 % Favored : 89.63 % 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: -0.56 (0.16), residues: 2424 helix: 0.40 (0.13), residues: 1496 sheet: -2.68 (0.40), residues: 124 loop : -1.29 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 593 HIS 0.008 0.001 HIS A 637 PHE 0.007 0.001 PHE A 574 TYR 0.010 0.001 TYR C 415 ARG 0.007 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 324 time to evaluate : 2.158 Fit side-chains REVERT: A 35 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7539 (ttt-90) REVERT: A 43 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7415 (tpp80) REVERT: A 119 THR cc_start: 0.8688 (p) cc_final: 0.8472 (t) REVERT: A 188 ASP cc_start: 0.8415 (t0) cc_final: 0.8203 (t0) REVERT: A 218 LEU cc_start: 0.8569 (tp) cc_final: 0.8234 (tt) REVERT: A 222 TYR cc_start: 0.7018 (m-80) cc_final: 0.6779 (m-80) REVERT: A 306 GLN cc_start: 0.8593 (mt0) cc_final: 0.8093 (mt0) REVERT: A 398 ILE cc_start: 0.9170 (mt) cc_final: 0.8890 (mt) REVERT: A 425 PHE cc_start: 0.8800 (m-80) cc_final: 0.8406 (m-80) REVERT: A 491 MET cc_start: 0.7915 (mmt) cc_final: 0.7651 (mmm) REVERT: B 35 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7548 (ttt-90) REVERT: B 43 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7437 (tpp80) REVERT: B 119 THR cc_start: 0.8694 (p) cc_final: 0.8464 (t) REVERT: B 188 ASP cc_start: 0.8441 (t0) cc_final: 0.8235 (t0) REVERT: B 214 GLN cc_start: 0.7836 (mp10) cc_final: 0.7555 (mp10) REVERT: B 218 LEU cc_start: 0.8554 (tp) cc_final: 0.8225 (tt) REVERT: B 222 TYR cc_start: 0.7054 (m-80) cc_final: 0.6820 (m-80) REVERT: B 306 GLN cc_start: 0.8605 (mt0) cc_final: 0.8103 (mt0) REVERT: B 398 ILE cc_start: 0.9168 (mt) cc_final: 0.8893 (mt) REVERT: B 425 PHE cc_start: 0.8820 (m-80) cc_final: 0.8426 (m-80) REVERT: B 491 MET cc_start: 0.7885 (mmt) cc_final: 0.7624 (mmm) REVERT: C 35 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7572 (ttt-90) REVERT: C 43 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7441 (tpp80) REVERT: C 119 THR cc_start: 0.8685 (p) cc_final: 0.8455 (t) REVERT: C 176 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7967 (mt-10) REVERT: C 188 ASP cc_start: 0.8434 (t0) cc_final: 0.8230 (t0) REVERT: C 214 GLN cc_start: 0.7840 (mp10) cc_final: 0.7557 (mp10) REVERT: C 218 LEU cc_start: 0.8559 (tp) cc_final: 0.8231 (tt) REVERT: C 222 TYR cc_start: 0.7052 (m-80) cc_final: 0.6822 (m-80) REVERT: C 306 GLN cc_start: 0.8596 (mt0) cc_final: 0.8095 (mt0) REVERT: C 398 ILE cc_start: 0.9150 (mt) cc_final: 0.8866 (mt) REVERT: C 425 PHE cc_start: 0.8807 (m-80) cc_final: 0.8425 (m-80) REVERT: C 491 MET cc_start: 0.7899 (mmt) cc_final: 0.7634 (mmm) REVERT: D 35 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7548 (ttt-90) REVERT: D 43 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7442 (tpp80) REVERT: D 119 THR cc_start: 0.8685 (p) cc_final: 0.8465 (t) REVERT: D 188 ASP cc_start: 0.8441 (t0) cc_final: 0.8231 (t0) REVERT: D 218 LEU cc_start: 0.8593 (tp) cc_final: 0.8254 (tt) REVERT: D 222 TYR cc_start: 0.7029 (m-80) cc_final: 0.6789 (m-80) REVERT: D 306 GLN cc_start: 0.8600 (mt0) cc_final: 0.8098 (mt0) REVERT: D 398 ILE cc_start: 0.9154 (mt) cc_final: 0.8870 (mt) REVERT: D 425 PHE cc_start: 0.8806 (m-80) cc_final: 0.8419 (m-80) REVERT: D 491 MET cc_start: 0.7915 (mmt) cc_final: 0.7646 (mmm) outliers start: 35 outliers final: 9 residues processed: 346 average time/residue: 0.2969 time to fit residues: 158.6947 Evaluate side-chains 301 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 288 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 206 GLN C 206 GLN D 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20592 Z= 0.225 Angle : 0.516 6.970 28016 Z= 0.253 Chirality : 0.038 0.146 3180 Planarity : 0.004 0.042 3468 Dihedral : 9.531 84.160 3412 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.14 % Allowed : 10.70 % Favored : 88.16 % 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: 0.04 (0.16), residues: 2424 helix: 0.94 (0.13), residues: 1504 sheet: -2.52 (0.42), residues: 124 loop : -1.21 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 593 HIS 0.008 0.001 HIS A 637 PHE 0.010 0.001 PHE B 468 TYR 0.008 0.001 TYR B 555 ARG 0.003 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 2.289 Fit side-chains REVERT: A 35 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7591 (ttt-90) REVERT: A 188 ASP cc_start: 0.8450 (t0) cc_final: 0.8210 (t0) REVERT: A 218 LEU cc_start: 0.8641 (tp) cc_final: 0.8334 (tt) REVERT: A 306 GLN cc_start: 0.8642 (mt0) cc_final: 0.8071 (mt0) REVERT: A 398 ILE cc_start: 0.9187 (mt) cc_final: 0.8926 (mt) REVERT: A 425 PHE cc_start: 0.8898 (m-80) cc_final: 0.8545 (m-80) REVERT: A 491 MET cc_start: 0.7937 (mmt) cc_final: 0.7655 (mmm) REVERT: B 35 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7608 (ttt-90) REVERT: B 188 ASP cc_start: 0.8446 (t0) cc_final: 0.8202 (t0) REVERT: B 218 LEU cc_start: 0.8644 (tp) cc_final: 0.8341 (tt) REVERT: B 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8101 (mt0) REVERT: B 398 ILE cc_start: 0.9188 (mt) cc_final: 0.8930 (mt) REVERT: B 425 PHE cc_start: 0.8904 (m-80) cc_final: 0.8545 (m-80) REVERT: B 491 MET cc_start: 0.7939 (mmt) cc_final: 0.7643 (mmm) REVERT: C 35 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7608 (ttt-90) REVERT: C 176 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7958 (mt-10) REVERT: C 188 ASP cc_start: 0.8445 (t0) cc_final: 0.8201 (t0) REVERT: C 306 GLN cc_start: 0.8645 (mt0) cc_final: 0.8099 (mt0) REVERT: C 398 ILE cc_start: 0.9188 (mt) cc_final: 0.8924 (mt) REVERT: C 425 PHE cc_start: 0.8903 (m-80) cc_final: 0.8553 (m-80) REVERT: C 491 MET cc_start: 0.7936 (mmt) cc_final: 0.7646 (mmm) REVERT: D 35 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7609 (ttt-90) REVERT: D 188 ASP cc_start: 0.8447 (t0) cc_final: 0.8203 (t0) REVERT: D 218 LEU cc_start: 0.8642 (tp) cc_final: 0.8330 (tt) REVERT: D 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8100 (mt0) REVERT: D 398 ILE cc_start: 0.9188 (mt) cc_final: 0.8925 (mt) REVERT: D 425 PHE cc_start: 0.8901 (m-80) cc_final: 0.8551 (m-80) REVERT: D 491 MET cc_start: 0.7940 (mmt) cc_final: 0.7649 (mmm) outliers start: 24 outliers final: 9 residues processed: 305 average time/residue: 0.2682 time to fit residues: 134.2967 Evaluate side-chains 275 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.7980 chunk 166 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.0670 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 0.0020 overall best weight: 0.5866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 206 GLN B 128 GLN B 206 GLN C 128 GLN C 206 GLN D 128 GLN D 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 20592 Z= 0.129 Angle : 0.466 6.947 28016 Z= 0.228 Chirality : 0.036 0.155 3180 Planarity : 0.003 0.041 3468 Dihedral : 9.291 89.593 3412 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.95 % Allowed : 11.84 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2424 helix: 1.38 (0.13), residues: 1500 sheet: -2.41 (0.41), residues: 124 loop : -1.09 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.009 0.001 HIS A 637 PHE 0.010 0.001 PHE C 531 TYR 0.008 0.001 TYR A 555 ARG 0.003 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 2.220 Fit side-chains REVERT: A 35 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7589 (ttt-90) REVERT: A 188 ASP cc_start: 0.8418 (t0) cc_final: 0.8136 (t0) REVERT: A 218 LEU cc_start: 0.8595 (tp) cc_final: 0.8297 (tt) REVERT: A 306 GLN cc_start: 0.8616 (mt0) cc_final: 0.8151 (mt0) REVERT: A 309 GLU cc_start: 0.7894 (tp30) cc_final: 0.7621 (tp30) REVERT: A 398 ILE cc_start: 0.9178 (mt) cc_final: 0.8908 (mt) REVERT: A 491 MET cc_start: 0.7925 (mmt) cc_final: 0.7641 (mmm) REVERT: B 35 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7601 (ttt-90) REVERT: B 188 ASP cc_start: 0.8422 (t0) cc_final: 0.8139 (t0) REVERT: B 218 LEU cc_start: 0.8598 (tp) cc_final: 0.8294 (tt) REVERT: B 306 GLN cc_start: 0.8621 (mt0) cc_final: 0.8151 (mt0) REVERT: B 309 GLU cc_start: 0.7879 (tp30) cc_final: 0.7605 (tp30) REVERT: B 398 ILE cc_start: 0.9180 (mt) cc_final: 0.8913 (mt) REVERT: B 491 MET cc_start: 0.7924 (mmt) cc_final: 0.7630 (mmm) REVERT: C 35 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7601 (ttt-90) REVERT: C 176 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7935 (mt-10) REVERT: C 188 ASP cc_start: 0.8414 (t0) cc_final: 0.8132 (t0) REVERT: C 306 GLN cc_start: 0.8621 (mt0) cc_final: 0.8152 (mt0) REVERT: C 309 GLU cc_start: 0.7875 (tp30) cc_final: 0.7607 (tp30) REVERT: C 398 ILE cc_start: 0.9174 (mt) cc_final: 0.8900 (mt) REVERT: C 491 MET cc_start: 0.7925 (mmt) cc_final: 0.7635 (mmm) REVERT: D 35 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7599 (ttt-90) REVERT: D 188 ASP cc_start: 0.8414 (t0) cc_final: 0.8133 (t0) REVERT: D 218 LEU cc_start: 0.8600 (tp) cc_final: 0.8308 (tt) REVERT: D 306 GLN cc_start: 0.8622 (mt0) cc_final: 0.8156 (mt0) REVERT: D 309 GLU cc_start: 0.7888 (tp30) cc_final: 0.7613 (tp30) REVERT: D 398 ILE cc_start: 0.9175 (mt) cc_final: 0.8903 (mt) REVERT: D 491 MET cc_start: 0.7927 (mmt) cc_final: 0.7636 (mmm) outliers start: 20 outliers final: 1 residues processed: 316 average time/residue: 0.2758 time to fit residues: 140.8792 Evaluate side-chains 280 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 275 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 35 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.0010 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 267 GLN B 206 GLN B 267 GLN C 206 GLN C 267 GLN D 206 GLN D 267 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20592 Z= 0.210 Angle : 0.490 6.933 28016 Z= 0.237 Chirality : 0.037 0.149 3180 Planarity : 0.003 0.039 3468 Dihedral : 9.110 77.498 3412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.33 % Allowed : 12.88 % Favored : 85.80 % 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: 0.76 (0.17), residues: 2424 helix: 1.58 (0.13), residues: 1500 sheet: -2.32 (0.42), residues: 124 loop : -1.07 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.009 0.001 HIS C 637 PHE 0.009 0.001 PHE D 468 TYR 0.007 0.001 TYR A 555 ARG 0.002 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 2.263 Fit side-chains REVERT: A 35 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7618 (ttt-90) REVERT: A 218 LEU cc_start: 0.8620 (tp) cc_final: 0.8300 (tt) REVERT: A 222 TYR cc_start: 0.6943 (m-80) cc_final: 0.6721 (m-80) REVERT: A 306 GLN cc_start: 0.8642 (mt0) cc_final: 0.8172 (mt0) REVERT: A 309 GLU cc_start: 0.7960 (tp30) cc_final: 0.7655 (tp30) REVERT: A 398 ILE cc_start: 0.9192 (mt) cc_final: 0.8935 (mt) REVERT: A 491 MET cc_start: 0.7966 (mmt) cc_final: 0.7666 (mmm) REVERT: B 35 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7600 (ttt-90) REVERT: B 218 LEU cc_start: 0.8599 (tp) cc_final: 0.8281 (tt) REVERT: B 306 GLN cc_start: 0.8647 (mt0) cc_final: 0.8174 (mt0) REVERT: B 309 GLU cc_start: 0.7962 (tp30) cc_final: 0.7659 (tp30) REVERT: B 398 ILE cc_start: 0.9197 (mt) cc_final: 0.8944 (mt) REVERT: B 491 MET cc_start: 0.7958 (mmt) cc_final: 0.7655 (mmm) REVERT: C 35 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7597 (ttt-90) REVERT: C 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8173 (mt0) REVERT: C 309 GLU cc_start: 0.7959 (tp30) cc_final: 0.7664 (tp30) REVERT: C 398 ILE cc_start: 0.9200 (mt) cc_final: 0.8936 (mt) REVERT: C 491 MET cc_start: 0.7962 (mmt) cc_final: 0.7667 (mmm) REVERT: D 35 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7602 (ttt-90) REVERT: D 215 MET cc_start: 0.8992 (mmm) cc_final: 0.8466 (mmm) REVERT: D 218 LEU cc_start: 0.8617 (tp) cc_final: 0.8292 (tt) REVERT: D 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8177 (mt0) REVERT: D 309 GLU cc_start: 0.7953 (tp30) cc_final: 0.7651 (tp30) REVERT: D 398 ILE cc_start: 0.9199 (mt) cc_final: 0.8934 (mt) REVERT: D 491 MET cc_start: 0.7963 (mmt) cc_final: 0.7663 (mmm) outliers start: 28 outliers final: 21 residues processed: 295 average time/residue: 0.2749 time to fit residues: 131.4521 Evaluate side-chains 285 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20592 Z= 0.199 Angle : 0.480 7.443 28016 Z= 0.232 Chirality : 0.037 0.150 3180 Planarity : 0.003 0.038 3468 Dihedral : 8.971 63.481 3412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.37 % Allowed : 12.69 % Favored : 85.94 % 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: 0.90 (0.17), residues: 2424 helix: 1.70 (0.13), residues: 1492 sheet: -2.19 (0.42), residues: 124 loop : -1.03 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.009 0.001 HIS C 637 PHE 0.008 0.001 PHE B 468 TYR 0.009 0.001 TYR C 415 ARG 0.002 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 2.394 Fit side-chains REVERT: A 35 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7616 (ttt-90) REVERT: A 218 LEU cc_start: 0.8630 (tp) cc_final: 0.8310 (tt) REVERT: A 222 TYR cc_start: 0.6915 (m-80) cc_final: 0.6684 (m-80) REVERT: A 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8166 (mt0) REVERT: A 309 GLU cc_start: 0.7942 (tp30) cc_final: 0.7636 (tp30) REVERT: A 398 ILE cc_start: 0.9205 (mt) cc_final: 0.8954 (mt) REVERT: A 491 MET cc_start: 0.7987 (mmt) cc_final: 0.7679 (mmm) REVERT: B 35 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: B 188 ASP cc_start: 0.8425 (t0) cc_final: 0.8115 (t0) REVERT: B 218 LEU cc_start: 0.8615 (tp) cc_final: 0.8322 (tt) REVERT: B 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8167 (mt0) REVERT: B 309 GLU cc_start: 0.7956 (tp30) cc_final: 0.7639 (tp30) REVERT: B 398 ILE cc_start: 0.9209 (mt) cc_final: 0.8962 (mt) REVERT: B 491 MET cc_start: 0.7976 (mmt) cc_final: 0.7668 (mmm) REVERT: C 35 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7626 (ttt-90) REVERT: C 188 ASP cc_start: 0.8433 (t0) cc_final: 0.8130 (t0) REVERT: C 306 GLN cc_start: 0.8649 (mt0) cc_final: 0.8170 (mt0) REVERT: C 309 GLU cc_start: 0.7954 (tp30) cc_final: 0.7645 (tp30) REVERT: C 398 ILE cc_start: 0.9203 (mt) cc_final: 0.8952 (mt) REVERT: C 491 MET cc_start: 0.7980 (mmt) cc_final: 0.7672 (mmm) REVERT: D 35 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7625 (ttt-90) REVERT: D 188 ASP cc_start: 0.8433 (t0) cc_final: 0.8121 (t0) REVERT: D 215 MET cc_start: 0.8999 (mmm) cc_final: 0.8475 (mmm) REVERT: D 218 LEU cc_start: 0.8635 (tp) cc_final: 0.8294 (tt) REVERT: D 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8169 (mt0) REVERT: D 309 GLU cc_start: 0.7963 (tp30) cc_final: 0.7645 (tp30) REVERT: D 398 ILE cc_start: 0.9204 (mt) cc_final: 0.8952 (mt) REVERT: D 491 MET cc_start: 0.7983 (mmt) cc_final: 0.7681 (mmm) outliers start: 29 outliers final: 20 residues processed: 294 average time/residue: 0.2782 time to fit residues: 134.6938 Evaluate side-chains 277 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 147 optimal weight: 0.3980 chunk 143 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20592 Z= 0.134 Angle : 0.450 6.914 28016 Z= 0.220 Chirality : 0.036 0.151 3180 Planarity : 0.003 0.037 3468 Dihedral : 8.756 58.410 3412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.33 % Allowed : 12.36 % Favored : 86.32 % 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: 1.11 (0.17), residues: 2424 helix: 1.89 (0.14), residues: 1492 sheet: -2.12 (0.41), residues: 124 loop : -0.97 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 593 HIS 0.009 0.001 HIS D 637 PHE 0.010 0.001 PHE B 478 TYR 0.007 0.001 TYR A 336 ARG 0.001 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 2.484 Fit side-chains REVERT: A 35 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7599 (ttt-90) REVERT: A 218 LEU cc_start: 0.8632 (tp) cc_final: 0.8300 (tt) REVERT: A 222 TYR cc_start: 0.6887 (m-80) cc_final: 0.6528 (m-80) REVERT: A 306 GLN cc_start: 0.8624 (mt0) cc_final: 0.8146 (mt0) REVERT: A 309 GLU cc_start: 0.7938 (tp30) cc_final: 0.7642 (tp30) REVERT: A 398 ILE cc_start: 0.9189 (mt) cc_final: 0.8927 (mt) REVERT: A 403 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 491 MET cc_start: 0.7977 (mmt) cc_final: 0.7648 (mmm) REVERT: B 35 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7613 (ttt-90) REVERT: B 188 ASP cc_start: 0.8400 (t0) cc_final: 0.8082 (t0) REVERT: B 218 LEU cc_start: 0.8612 (tp) cc_final: 0.8303 (tt) REVERT: B 306 GLN cc_start: 0.8627 (mt0) cc_final: 0.8146 (mt0) REVERT: B 309 GLU cc_start: 0.7951 (tp30) cc_final: 0.7652 (tp30) REVERT: B 398 ILE cc_start: 0.9193 (mt) cc_final: 0.8936 (mt) REVERT: B 491 MET cc_start: 0.7970 (mmt) cc_final: 0.7643 (mmm) REVERT: C 35 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7618 (ttt-90) REVERT: C 306 GLN cc_start: 0.8625 (mt0) cc_final: 0.8146 (mt0) REVERT: C 309 GLU cc_start: 0.7951 (tp30) cc_final: 0.7656 (tp30) REVERT: C 398 ILE cc_start: 0.9188 (mt) cc_final: 0.8925 (mt) REVERT: C 403 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7258 (mm-30) REVERT: C 491 MET cc_start: 0.7974 (mmt) cc_final: 0.7650 (mmm) REVERT: D 35 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7614 (ttt-90) REVERT: D 218 LEU cc_start: 0.8617 (tp) cc_final: 0.8335 (tt) REVERT: D 306 GLN cc_start: 0.8626 (mt0) cc_final: 0.8146 (mt0) REVERT: D 309 GLU cc_start: 0.7957 (tp30) cc_final: 0.7648 (tp30) REVERT: D 398 ILE cc_start: 0.9188 (mt) cc_final: 0.8925 (mt) REVERT: D 403 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 491 MET cc_start: 0.7977 (mmt) cc_final: 0.7652 (mmm) outliers start: 28 outliers final: 16 residues processed: 282 average time/residue: 0.2704 time to fit residues: 124.6836 Evaluate side-chains 271 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN D 128 GLN D 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20592 Z= 0.183 Angle : 0.467 6.926 28016 Z= 0.227 Chirality : 0.036 0.149 3180 Planarity : 0.003 0.036 3468 Dihedral : 8.671 59.537 3412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.33 % Allowed : 12.59 % Favored : 86.08 % 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: 1.13 (0.17), residues: 2424 helix: 1.89 (0.14), residues: 1492 sheet: -2.02 (0.43), residues: 124 loop : -0.96 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 593 HIS 0.009 0.001 HIS D 637 PHE 0.010 0.001 PHE A 478 TYR 0.008 0.001 TYR C 415 ARG 0.001 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 2.447 Fit side-chains REVERT: A 35 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7614 (ttt-90) REVERT: A 188 ASP cc_start: 0.8362 (t0) cc_final: 0.8033 (t0) REVERT: A 218 LEU cc_start: 0.8647 (tp) cc_final: 0.8311 (tt) REVERT: A 222 TYR cc_start: 0.6882 (m-80) cc_final: 0.6508 (m-80) REVERT: A 306 GLN cc_start: 0.8657 (mt0) cc_final: 0.8184 (mt0) REVERT: A 309 GLU cc_start: 0.7937 (tp30) cc_final: 0.7641 (tp30) REVERT: A 398 ILE cc_start: 0.9203 (mt) cc_final: 0.8951 (mt) REVERT: A 403 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 491 MET cc_start: 0.7989 (mmt) cc_final: 0.7659 (mmm) REVERT: B 35 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7619 (ttt-90) REVERT: B 218 LEU cc_start: 0.8650 (tp) cc_final: 0.8341 (tt) REVERT: B 306 GLN cc_start: 0.8659 (mt0) cc_final: 0.8182 (mt0) REVERT: B 309 GLU cc_start: 0.7978 (tp30) cc_final: 0.7679 (tp30) REVERT: B 398 ILE cc_start: 0.9203 (mt) cc_final: 0.8952 (mt) REVERT: B 491 MET cc_start: 0.7981 (mmt) cc_final: 0.7659 (mmm) REVERT: C 35 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7625 (ttt-90) REVERT: C 188 ASP cc_start: 0.8395 (t0) cc_final: 0.8085 (t0) REVERT: C 215 MET cc_start: 0.9014 (mmm) cc_final: 0.8620 (mmm) REVERT: C 306 GLN cc_start: 0.8656 (mt0) cc_final: 0.8163 (mt0) REVERT: C 309 GLU cc_start: 0.7981 (tp30) cc_final: 0.7685 (tp30) REVERT: C 398 ILE cc_start: 0.9202 (mt) cc_final: 0.8950 (mt) REVERT: C 403 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7252 (mm-30) REVERT: C 491 MET cc_start: 0.7983 (mmt) cc_final: 0.7653 (mmm) REVERT: D 35 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: D 188 ASP cc_start: 0.8375 (t0) cc_final: 0.8040 (t0) REVERT: D 218 LEU cc_start: 0.8645 (tp) cc_final: 0.8347 (tt) REVERT: D 306 GLN cc_start: 0.8659 (mt0) cc_final: 0.8183 (mt0) REVERT: D 309 GLU cc_start: 0.7996 (tp30) cc_final: 0.7687 (tp30) REVERT: D 398 ILE cc_start: 0.9203 (mt) cc_final: 0.8951 (mt) REVERT: D 403 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7254 (mm-30) REVERT: D 491 MET cc_start: 0.7980 (mmt) cc_final: 0.7655 (mmm) outliers start: 28 outliers final: 19 residues processed: 276 average time/residue: 0.2882 time to fit residues: 129.8896 Evaluate side-chains 273 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20592 Z= 0.176 Angle : 0.464 7.684 28016 Z= 0.225 Chirality : 0.036 0.149 3180 Planarity : 0.003 0.036 3468 Dihedral : 8.573 59.667 3412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.56 % Allowed : 12.59 % Favored : 85.84 % 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: 1.21 (0.17), residues: 2424 helix: 1.93 (0.13), residues: 1496 sheet: -2.00 (0.43), residues: 124 loop : -0.88 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.009 0.001 HIS D 637 PHE 0.007 0.001 PHE A 468 TYR 0.010 0.001 TYR A 336 ARG 0.001 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 2.403 Fit side-chains REVERT: A 35 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7611 (ttt-90) REVERT: A 218 LEU cc_start: 0.8651 (tp) cc_final: 0.8314 (tt) REVERT: A 222 TYR cc_start: 0.6872 (m-80) cc_final: 0.6497 (m-80) REVERT: A 306 GLN cc_start: 0.8658 (mt0) cc_final: 0.8184 (mt0) REVERT: A 309 GLU cc_start: 0.7967 (tp30) cc_final: 0.7670 (tp30) REVERT: A 398 ILE cc_start: 0.9201 (mt) cc_final: 0.8961 (mt) REVERT: A 403 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 491 MET cc_start: 0.7998 (mmt) cc_final: 0.7668 (mmm) REVERT: B 35 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7618 (ttt-90) REVERT: B 188 ASP cc_start: 0.8372 (t0) cc_final: 0.8062 (t0) REVERT: B 218 LEU cc_start: 0.8644 (tp) cc_final: 0.8327 (tt) REVERT: B 306 GLN cc_start: 0.8663 (mt0) cc_final: 0.8186 (mt0) REVERT: B 309 GLU cc_start: 0.7961 (tp30) cc_final: 0.7657 (tp30) REVERT: B 398 ILE cc_start: 0.9199 (mt) cc_final: 0.8951 (mt) REVERT: B 491 MET cc_start: 0.7987 (mmt) cc_final: 0.7659 (mmm) REVERT: C 35 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7624 (ttt-90) REVERT: C 306 GLN cc_start: 0.8660 (mt0) cc_final: 0.8172 (mt0) REVERT: C 309 GLU cc_start: 0.7960 (tp30) cc_final: 0.7659 (tp30) REVERT: C 398 ILE cc_start: 0.9200 (mt) cc_final: 0.8950 (mt) REVERT: C 403 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7226 (mm-30) REVERT: C 491 MET cc_start: 0.7988 (mmt) cc_final: 0.7664 (mmm) REVERT: D 35 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: D 218 LEU cc_start: 0.8642 (tp) cc_final: 0.8349 (tt) REVERT: D 306 GLN cc_start: 0.8659 (mt0) cc_final: 0.8168 (mt0) REVERT: D 309 GLU cc_start: 0.7978 (tp30) cc_final: 0.7664 (tp30) REVERT: D 398 ILE cc_start: 0.9199 (mt) cc_final: 0.8950 (mt) REVERT: D 403 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 491 MET cc_start: 0.7992 (mmt) cc_final: 0.7666 (mmm) outliers start: 33 outliers final: 25 residues processed: 281 average time/residue: 0.2698 time to fit residues: 124.7971 Evaluate side-chains 281 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20592 Z= 0.147 Angle : 0.461 8.211 28016 Z= 0.224 Chirality : 0.036 0.150 3180 Planarity : 0.003 0.036 3468 Dihedral : 8.454 59.766 3412 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.33 % Allowed : 13.30 % Favored : 85.37 % 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: 1.25 (0.17), residues: 2424 helix: 1.96 (0.14), residues: 1496 sheet: -1.96 (0.42), residues: 124 loop : -0.86 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.009 0.001 HIS D 637 PHE 0.007 0.001 PHE B 416 TYR 0.011 0.001 TYR A 336 ARG 0.001 0.000 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 2.157 Fit side-chains REVERT: A 35 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7613 (ttt-90) REVERT: A 188 ASP cc_start: 0.8319 (t0) cc_final: 0.7984 (t0) REVERT: A 218 LEU cc_start: 0.8646 (tp) cc_final: 0.8360 (tt) REVERT: A 306 GLN cc_start: 0.8633 (mt0) cc_final: 0.8172 (mt0) REVERT: A 309 GLU cc_start: 0.7968 (tp30) cc_final: 0.7664 (tp30) REVERT: A 398 ILE cc_start: 0.9201 (mt) cc_final: 0.8946 (mt) REVERT: A 403 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 491 MET cc_start: 0.7965 (mmt) cc_final: 0.7604 (mmm) REVERT: B 35 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7618 (ttt-90) REVERT: B 218 LEU cc_start: 0.8655 (tp) cc_final: 0.8345 (tt) REVERT: B 306 GLN cc_start: 0.8652 (mt0) cc_final: 0.8155 (mt0) REVERT: B 309 GLU cc_start: 0.7954 (tp30) cc_final: 0.7651 (tp30) REVERT: B 398 ILE cc_start: 0.9196 (mt) cc_final: 0.8944 (mt) REVERT: B 491 MET cc_start: 0.7974 (mmt) cc_final: 0.7640 (mmm) REVERT: C 35 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7623 (ttt-90) REVERT: C 188 ASP cc_start: 0.8361 (t0) cc_final: 0.8050 (t0) REVERT: C 306 GLN cc_start: 0.8657 (mt0) cc_final: 0.8163 (mt0) REVERT: C 309 GLU cc_start: 0.7954 (tp30) cc_final: 0.7655 (tp30) REVERT: C 398 ILE cc_start: 0.9201 (mt) cc_final: 0.8946 (mt) REVERT: C 403 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7219 (mm-30) REVERT: C 491 MET cc_start: 0.7979 (mmt) cc_final: 0.7657 (mmm) REVERT: D 35 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7621 (ttt-90) REVERT: D 188 ASP cc_start: 0.8321 (t0) cc_final: 0.7986 (t0) REVERT: D 218 LEU cc_start: 0.8646 (tp) cc_final: 0.8358 (tt) REVERT: D 306 GLN cc_start: 0.8651 (mt0) cc_final: 0.8155 (mt0) REVERT: D 309 GLU cc_start: 0.7963 (tp30) cc_final: 0.7646 (tp30) REVERT: D 398 ILE cc_start: 0.9201 (mt) cc_final: 0.8945 (mt) REVERT: D 403 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 491 MET cc_start: 0.7980 (mmt) cc_final: 0.7656 (mmm) outliers start: 28 outliers final: 19 residues processed: 283 average time/residue: 0.2935 time to fit residues: 131.7083 Evaluate side-chains 271 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 84 HIS B 418 GLN C 128 GLN C 418 GLN D 84 HIS D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097262 restraints weight = 28850.728| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.23 r_work: 0.2991 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 20592 Z= 0.529 Angle : 0.671 7.204 28016 Z= 0.327 Chirality : 0.044 0.166 3180 Planarity : 0.004 0.035 3468 Dihedral : 8.849 64.038 3412 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.37 % Allowed : 13.49 % Favored : 85.13 % 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: 0.69 (0.17), residues: 2424 helix: 1.42 (0.13), residues: 1500 sheet: -1.11 (0.60), residues: 84 loop : -1.12 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 495 HIS 0.009 0.001 HIS D 637 PHE 0.018 0.002 PHE B 425 TYR 0.018 0.002 TYR B 526 ARG 0.003 0.001 ARG D 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.28 seconds wall clock time: 80 minutes 37.54 seconds (4837.54 seconds total)