Starting phenix.real_space_refine on Sat Feb 17 20:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0m_24109/02_2024/7n0m_24109_updated.pdb" } resolution = 3.5 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= 0.030 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 B 4 2.79 5 C 12988 2.51 5 N 3304 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 77": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D GLU 670": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19780 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "D" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4928 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.78, per 1000 atoms: 0.54 Number of scatterers: 19780 At special positions: 0 Unit cell: (142.31, 142.31, 115.56, 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 108 16.00 O 3376 8.00 N 3304 7.00 C 12988 6.00 B 4 5.00 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: 7.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 4 sheets defined 53.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.954A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.506A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.063A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.774A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.621A pdb=" N ALA A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 removed outlier: 3.757A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.585A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 412 removed outlier: 3.565A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 462 through 465 No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.586A pdb=" N VAL A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 4.714A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.655A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 558 removed outlier: 4.219A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 Processing helix chain 'A' and resid 620 through 649 removed outlier: 4.355A pdb=" N ILE A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.218A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.954A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.506A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.063A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.774A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.621A pdb=" N ALA B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 removed outlier: 3.756A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.585A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 412 removed outlier: 3.565A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.585A pdb=" N VAL B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 518 removed outlier: 4.714A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.655A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 558 removed outlier: 4.219A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 599 Processing helix chain 'B' and resid 620 through 649 removed outlier: 4.355A pdb=" N ILE B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 673 removed outlier: 4.217A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 removed outlier: 3.953A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.506A pdb=" N ILE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 4.063A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.775A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.621A pdb=" N ALA C 302 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.757A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.585A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 412 removed outlier: 3.565A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.586A pdb=" N VAL C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 518 removed outlier: 4.714A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 531 removed outlier: 3.655A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 558 removed outlier: 4.219A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 599 Processing helix chain 'C' and resid 620 through 649 removed outlier: 4.355A pdb=" N ILE C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 673 removed outlier: 4.217A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.954A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.506A pdb=" N ILE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 186 removed outlier: 4.063A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 263 through 281 removed outlier: 3.775A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 304 removed outlier: 3.621A pdb=" N ALA D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.757A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.585A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 412 removed outlier: 3.565A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 462 through 465 No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.586A pdb=" N VAL D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 518 removed outlier: 4.714A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 removed outlier: 3.654A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 558 removed outlier: 4.220A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 599 Processing helix chain 'D' and resid 620 through 649 removed outlier: 4.354A pdb=" N ILE D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 646 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 673 removed outlier: 4.218A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.530A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 333 through 335 removed outlier: 3.529A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5706 1.33 - 1.45: 3684 1.45 - 1.57: 10726 1.57 - 1.69: 8 1.69 - 1.81: 164 Bond restraints: 20288 Sorted by residual: bond pdb=" CG LEU B 342 " pdb=" CD1 LEU B 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CG LEU D 342 " pdb=" CD1 LEU D 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.48e+00 bond pdb=" CG LEU A 342 " pdb=" CD1 LEU A 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CG LEU C 342 " pdb=" CD1 LEU C 342 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CB MET A 404 " pdb=" CG MET A 404 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 ... (remaining 20283 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.88: 242 103.88 - 111.44: 8795 111.44 - 118.99: 7585 118.99 - 126.54: 10543 126.54 - 134.10: 411 Bond angle restraints: 27576 Sorted by residual: angle pdb=" N VAL C 348 " pdb=" CA VAL C 348 " pdb=" C VAL C 348 " ideal model delta sigma weight residual 113.53 107.66 5.87 9.80e-01 1.04e+00 3.59e+01 angle pdb=" N VAL B 348 " pdb=" CA VAL B 348 " pdb=" C VAL B 348 " ideal model delta sigma weight residual 113.53 107.66 5.87 9.80e-01 1.04e+00 3.58e+01 angle pdb=" N VAL A 348 " pdb=" CA VAL A 348 " pdb=" C VAL A 348 " ideal model delta sigma weight residual 113.53 107.67 5.86 9.80e-01 1.04e+00 3.57e+01 angle pdb=" N VAL D 348 " pdb=" CA VAL D 348 " pdb=" C VAL D 348 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.55e+01 angle pdb=" CB MET B 404 " pdb=" CG MET B 404 " pdb=" SD MET B 404 " ideal model delta sigma weight residual 112.70 97.64 15.06 3.00e+00 1.11e-01 2.52e+01 ... (remaining 27571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 10333 16.57 - 33.15: 1147 33.15 - 49.72: 272 49.72 - 66.30: 44 66.30 - 82.87: 32 Dihedral angle restraints: 11828 sinusoidal: 4600 harmonic: 7228 Sorted by residual: dihedral pdb=" CA PRO B 699 " pdb=" C PRO B 699 " pdb=" N ASP B 700 " pdb=" CA ASP B 700 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO D 699 " pdb=" C PRO D 699 " pdb=" N ASP D 700 " pdb=" CA ASP D 700 " ideal model delta harmonic sigma weight residual 180.00 155.91 24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO C 699 " pdb=" C PRO C 699 " pdb=" N ASP C 700 " pdb=" CA ASP C 700 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 11825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2046 0.046 - 0.091: 793 0.091 - 0.137: 244 0.137 - 0.182: 49 0.182 - 0.228: 12 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB VAL B 84 " pdb=" CA VAL B 84 " pdb=" CG1 VAL B 84 " pdb=" CG2 VAL B 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL D 84 " pdb=" CA VAL D 84 " pdb=" CG1 VAL D 84 " pdb=" CG2 VAL D 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL A 84 " pdb=" CA VAL A 84 " pdb=" CG1 VAL A 84 " pdb=" CG2 VAL A 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3141 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 162 " -0.019 2.00e-02 2.50e+03 2.00e-02 8.00e+00 pdb=" CG TYR B 162 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 162 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 162 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 162 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 162 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 162 " 0.019 2.00e-02 2.50e+03 2.00e-02 7.97e+00 pdb=" CG TYR D 162 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 162 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 162 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 162 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 162 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 162 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 162 " -0.019 2.00e-02 2.50e+03 2.00e-02 7.96e+00 pdb=" CG TYR C 162 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR C 162 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 162 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 162 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 162 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 162 " 0.003 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5766 2.81 - 3.33: 18593 3.33 - 3.86: 32610 3.86 - 4.38: 36206 4.38 - 4.90: 62321 Nonbonded interactions: 155496 Sorted by model distance: nonbonded pdb=" O PHE D 209 " pdb=" OG SER D 215 " model vdw 2.290 2.440 nonbonded pdb=" O PHE A 209 " pdb=" OG SER A 215 " model vdw 2.291 2.440 nonbonded pdb=" O PHE C 209 " pdb=" OG SER C 215 " model vdw 2.291 2.440 nonbonded pdb=" O PHE B 209 " pdb=" OG SER B 215 " model vdw 2.291 2.440 nonbonded pdb=" NE2 GLN C 452 " pdb=" OE2 GLU C 473 " model vdw 2.337 2.520 ... (remaining 155491 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 74 through 729) selection = chain 'B' selection = (chain 'C' and resid 74 through 729) selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 52.010 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.084 20288 Z= 0.565 Angle : 1.056 15.064 27576 Z= 0.537 Chirality : 0.054 0.228 3144 Planarity : 0.006 0.070 3396 Dihedral : 15.230 82.869 7164 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 0.76 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.15), residues: 2452 helix: -1.05 (0.13), residues: 1388 sheet: 0.32 (0.66), residues: 64 loop : -3.04 (0.15), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 660 HIS 0.023 0.003 HIS A 165 PHE 0.038 0.003 PHE C 472 TYR 0.049 0.003 TYR B 162 ARG 0.004 0.001 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 2.572 Fit side-chains REVERT: A 145 ASP cc_start: 0.6662 (m-30) cc_final: 0.6210 (m-30) REVERT: A 457 TRP cc_start: 0.8212 (t60) cc_final: 0.7797 (t60) REVERT: B 141 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7423 (tp-100) REVERT: B 145 ASP cc_start: 0.7040 (m-30) cc_final: 0.6572 (m-30) REVERT: B 457 TRP cc_start: 0.7990 (t60) cc_final: 0.7641 (t60) REVERT: B 511 ASN cc_start: 0.8672 (m-40) cc_final: 0.8442 (m-40) REVERT: C 141 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7685 (tp-100) REVERT: C 145 ASP cc_start: 0.6968 (m-30) cc_final: 0.6541 (m-30) REVERT: C 457 TRP cc_start: 0.8018 (t60) cc_final: 0.7670 (t60) REVERT: D 141 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7730 (tp-100) REVERT: D 145 ASP cc_start: 0.6944 (m-30) cc_final: 0.6515 (m-30) REVERT: D 457 TRP cc_start: 0.8012 (t60) cc_final: 0.7645 (t60) outliers start: 12 outliers final: 4 residues processed: 205 average time/residue: 0.2789 time to fit residues: 93.0362 Evaluate side-chains 146 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.3980 chunk 184 optimal weight: 0.0980 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS C 521 HIS D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20288 Z= 0.148 Angle : 0.567 10.829 27576 Z= 0.264 Chirality : 0.036 0.116 3144 Planarity : 0.004 0.055 3396 Dihedral : 6.499 63.572 2716 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.72 % Allowed : 8.08 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.27 (0.16), residues: 2452 helix: 0.31 (0.14), residues: 1392 sheet: 0.29 (0.64), residues: 72 loop : -2.69 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 660 HIS 0.004 0.001 HIS C 521 PHE 0.018 0.001 PHE D 476 TYR 0.019 0.001 TYR B 162 ARG 0.002 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.391 Fit side-chains REVERT: A 141 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7148 (tp-100) REVERT: A 457 TRP cc_start: 0.8020 (t60) cc_final: 0.7741 (t60) REVERT: B 141 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7544 (tp-100) REVERT: B 145 ASP cc_start: 0.6981 (m-30) cc_final: 0.6522 (m-30) REVERT: B 457 TRP cc_start: 0.7861 (t60) cc_final: 0.7600 (t60) REVERT: B 511 ASN cc_start: 0.8562 (m-40) cc_final: 0.8256 (m-40) REVERT: C 145 ASP cc_start: 0.6859 (m-30) cc_final: 0.6404 (m-30) REVERT: C 457 TRP cc_start: 0.7867 (t60) cc_final: 0.7605 (t60) REVERT: C 511 ASN cc_start: 0.8610 (m-40) cc_final: 0.8259 (m-40) REVERT: D 457 TRP cc_start: 0.7823 (t60) cc_final: 0.7569 (t60) outliers start: 15 outliers final: 12 residues processed: 215 average time/residue: 0.2887 time to fit residues: 101.4172 Evaluate side-chains 176 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 0.0170 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20288 Z= 0.234 Angle : 0.580 7.335 27576 Z= 0.278 Chirality : 0.038 0.119 3144 Planarity : 0.004 0.059 3396 Dihedral : 5.881 55.365 2716 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.06 % Allowed : 11.09 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.75 (0.17), residues: 2452 helix: 0.74 (0.14), residues: 1400 sheet: 0.33 (0.64), residues: 72 loop : -2.49 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 386 HIS 0.010 0.001 HIS A 521 PHE 0.012 0.001 PHE C 705 TYR 0.017 0.001 TYR B 162 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 2.386 Fit side-chains REVERT: A 141 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7454 (tp-100) REVERT: A 457 TRP cc_start: 0.8144 (t60) cc_final: 0.7736 (t60) REVERT: A 521 HIS cc_start: 0.5666 (OUTLIER) cc_final: 0.4377 (p90) REVERT: B 141 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7525 (tp-100) REVERT: B 145 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: B 457 TRP cc_start: 0.8042 (t60) cc_final: 0.7674 (t60) REVERT: B 521 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.4638 (p-80) REVERT: C 141 GLN cc_start: 0.7776 (tp-100) cc_final: 0.6957 (tp-100) REVERT: C 457 TRP cc_start: 0.8061 (t60) cc_final: 0.7664 (t60) REVERT: C 521 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.4442 (p90) REVERT: C 607 MET cc_start: 0.8103 (tpt) cc_final: 0.7865 (tpt) REVERT: D 141 GLN cc_start: 0.7760 (tp-100) cc_final: 0.6943 (tp-100) REVERT: D 145 ASP cc_start: 0.6818 (m-30) cc_final: 0.6328 (m-30) REVERT: D 457 TRP cc_start: 0.8018 (t60) cc_final: 0.7619 (t60) outliers start: 43 outliers final: 26 residues processed: 196 average time/residue: 0.2578 time to fit residues: 85.0172 Evaluate side-chains 189 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 0.0170 chunk 222 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 20288 Z= 0.229 Angle : 0.555 7.160 27576 Z= 0.267 Chirality : 0.037 0.121 3144 Planarity : 0.004 0.057 3396 Dihedral : 5.470 51.898 2716 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.58 % Allowed : 13.15 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.52 (0.17), residues: 2452 helix: 0.96 (0.15), residues: 1400 sheet: 0.33 (0.65), residues: 72 loop : -2.44 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 386 HIS 0.004 0.001 HIS D 169 PHE 0.011 0.001 PHE D 705 TYR 0.015 0.001 TYR B 471 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 157 time to evaluate : 2.097 Fit side-chains REVERT: A 141 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7457 (tp-100) REVERT: A 457 TRP cc_start: 0.8132 (t60) cc_final: 0.7669 (t60) REVERT: B 141 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7507 (tp-100) REVERT: B 145 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: B 457 TRP cc_start: 0.8067 (t60) cc_final: 0.7614 (t60) REVERT: C 141 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7617 (tp40) REVERT: C 457 TRP cc_start: 0.8036 (t60) cc_final: 0.7559 (t60) REVERT: C 521 HIS cc_start: 0.5621 (OUTLIER) cc_final: 0.4026 (p90) REVERT: C 607 MET cc_start: 0.8090 (tpt) cc_final: 0.7875 (tpt) REVERT: D 141 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7009 (tp-100) REVERT: D 145 ASP cc_start: 0.6913 (m-30) cc_final: 0.6536 (m-30) REVERT: D 457 TRP cc_start: 0.7979 (t60) cc_final: 0.7499 (t60) outliers start: 54 outliers final: 31 residues processed: 196 average time/residue: 0.2713 time to fit residues: 87.5415 Evaluate side-chains 184 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN D 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 20288 Z= 0.467 Angle : 0.715 7.886 27576 Z= 0.347 Chirality : 0.042 0.144 3144 Planarity : 0.004 0.066 3396 Dihedral : 5.522 46.848 2716 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.63 % Allowed : 14.44 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2452 helix: 0.55 (0.14), residues: 1416 sheet: 0.03 (0.64), residues: 72 loop : -2.48 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 660 HIS 0.009 0.001 HIS A 169 PHE 0.023 0.002 PHE D 397 TYR 0.022 0.002 TYR C 228 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 158 time to evaluate : 2.317 Fit side-chains REVERT: A 141 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7552 (tp-100) REVERT: A 510 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 521 HIS cc_start: 0.5873 (OUTLIER) cc_final: 0.5048 (p-80) REVERT: B 141 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7536 (tp-100) REVERT: B 145 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: B 521 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.4765 (p-80) REVERT: C 141 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7356 (tp-100) REVERT: C 521 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.4756 (p90) REVERT: D 141 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7283 (tp-100) REVERT: D 145 ASP cc_start: 0.7057 (m-30) cc_final: 0.6623 (m-30) REVERT: D 521 HIS cc_start: 0.5781 (OUTLIER) cc_final: 0.4398 (p-80) outliers start: 76 outliers final: 45 residues processed: 216 average time/residue: 0.2547 time to fit residues: 92.5395 Evaluate side-chains 185 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 689 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 236 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20288 Z= 0.161 Angle : 0.549 7.960 27576 Z= 0.257 Chirality : 0.036 0.132 3144 Planarity : 0.004 0.059 3396 Dihedral : 5.041 51.995 2716 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.25 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.35 (0.17), residues: 2452 helix: 1.10 (0.15), residues: 1396 sheet: 0.28 (0.64), residues: 72 loop : -2.34 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.003 0.001 HIS C 521 PHE 0.010 0.001 PHE B 705 TYR 0.015 0.001 TYR D 471 ARG 0.002 0.000 ARG D 706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 159 time to evaluate : 2.573 Fit side-chains REVERT: A 141 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7665 (tp-100) REVERT: B 141 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7547 (tp-100) REVERT: B 145 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6530 (m-30) REVERT: B 457 TRP cc_start: 0.8075 (t60) cc_final: 0.7744 (t60) REVERT: B 521 HIS cc_start: 0.5416 (OUTLIER) cc_final: 0.4433 (p-80) REVERT: B 607 MET cc_start: 0.8018 (tpt) cc_final: 0.7779 (tpt) REVERT: C 141 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7359 (tp-100) REVERT: C 457 TRP cc_start: 0.8056 (t60) cc_final: 0.7748 (t60) REVERT: C 521 HIS cc_start: 0.5489 (OUTLIER) cc_final: 0.4127 (p90) REVERT: D 141 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7186 (tp-100) REVERT: D 145 ASP cc_start: 0.6969 (m-30) cc_final: 0.6475 (m-30) REVERT: D 457 TRP cc_start: 0.8033 (t60) cc_final: 0.7727 (t60) outliers start: 68 outliers final: 35 residues processed: 213 average time/residue: 0.2632 time to fit residues: 94.5605 Evaluate side-chains 194 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 TRP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 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 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20288 Z= 0.227 Angle : 0.581 8.350 27576 Z= 0.272 Chirality : 0.037 0.126 3144 Planarity : 0.004 0.058 3396 Dihedral : 4.991 51.260 2716 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.06 % Allowed : 16.83 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.31 (0.17), residues: 2452 helix: 1.09 (0.14), residues: 1420 sheet: 0.22 (0.64), residues: 72 loop : -2.32 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.004 0.001 HIS C 521 PHE 0.011 0.001 PHE A 705 TYR 0.013 0.001 TYR D 162 ARG 0.002 0.000 ARG D 706 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 152 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 TRP cc_start: 0.8083 (t60) cc_final: 0.7749 (t60) REVERT: A 521 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4418 (p-80) REVERT: B 141 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7560 (tp-100) REVERT: B 145 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: B 457 TRP cc_start: 0.8067 (t60) cc_final: 0.7739 (t60) REVERT: B 521 HIS cc_start: 0.5392 (OUTLIER) cc_final: 0.4443 (p-80) REVERT: B 607 MET cc_start: 0.8036 (tpt) cc_final: 0.7774 (tpt) REVERT: C 141 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7577 (tp-100) REVERT: C 457 TRP cc_start: 0.8066 (t60) cc_final: 0.7743 (t60) REVERT: C 521 HIS cc_start: 0.5363 (OUTLIER) cc_final: 0.4240 (p90) REVERT: D 141 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7108 (tp-100) REVERT: D 145 ASP cc_start: 0.6985 (m-30) cc_final: 0.6583 (m-30) REVERT: D 457 TRP cc_start: 0.8007 (t60) cc_final: 0.7686 (t60) REVERT: D 521 HIS cc_start: 0.5371 (OUTLIER) cc_final: 0.3901 (p-80) outliers start: 64 outliers final: 43 residues processed: 203 average time/residue: 0.2549 time to fit residues: 86.3194 Evaluate side-chains 196 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 191 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20288 Z= 0.249 Angle : 0.598 9.813 27576 Z= 0.280 Chirality : 0.038 0.122 3144 Planarity : 0.004 0.058 3396 Dihedral : 4.993 50.721 2716 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.72 % Allowed : 16.83 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.32 (0.17), residues: 2452 helix: 1.05 (0.14), residues: 1424 sheet: 0.23 (0.64), residues: 72 loop : -2.28 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 660 HIS 0.004 0.001 HIS C 169 PHE 0.014 0.001 PHE A 705 TYR 0.013 0.001 TYR C 162 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 155 time to evaluate : 2.308 Fit side-chains REVERT: A 457 TRP cc_start: 0.8081 (t60) cc_final: 0.7736 (t60) REVERT: A 521 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.4544 (p-80) REVERT: B 141 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7548 (tp-100) REVERT: B 145 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6460 (m-30) REVERT: B 457 TRP cc_start: 0.8058 (t60) cc_final: 0.7736 (t60) REVERT: B 521 HIS cc_start: 0.5498 (OUTLIER) cc_final: 0.4470 (p-80) REVERT: B 607 MET cc_start: 0.8071 (tpt) cc_final: 0.7794 (tpt) REVERT: C 141 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7333 (tp-100) REVERT: C 457 TRP cc_start: 0.8054 (t60) cc_final: 0.7733 (t60) REVERT: C 521 HIS cc_start: 0.5578 (OUTLIER) cc_final: 0.4379 (p90) REVERT: D 141 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7263 (tp-100) REVERT: D 145 ASP cc_start: 0.7013 (m-30) cc_final: 0.6498 (m-30) REVERT: D 457 TRP cc_start: 0.7994 (t60) cc_final: 0.7677 (t60) REVERT: D 521 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4136 (p-80) outliers start: 57 outliers final: 41 residues processed: 200 average time/residue: 0.2551 time to fit residues: 85.1712 Evaluate side-chains 198 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 191 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20288 Z= 0.147 Angle : 0.541 8.103 27576 Z= 0.249 Chirality : 0.036 0.129 3144 Planarity : 0.003 0.055 3396 Dihedral : 4.762 53.387 2716 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.34 % Allowed : 17.50 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.02 (0.18), residues: 2452 helix: 1.42 (0.15), residues: 1392 sheet: 0.25 (0.64), residues: 72 loop : -2.18 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.003 0.001 HIS C 521 PHE 0.011 0.001 PHE D 705 TYR 0.011 0.001 TYR C 471 ARG 0.002 0.000 ARG D 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 2.591 Fit side-chains REVERT: A 457 TRP cc_start: 0.7980 (t60) cc_final: 0.7692 (t60) REVERT: A 511 ASN cc_start: 0.8584 (m-40) cc_final: 0.8114 (m-40) REVERT: A 521 HIS cc_start: 0.5107 (OUTLIER) cc_final: 0.4289 (p-80) REVERT: B 141 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7452 (tp-100) REVERT: B 145 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: B 457 TRP cc_start: 0.7979 (t60) cc_final: 0.7689 (t60) REVERT: C 457 TRP cc_start: 0.7978 (t60) cc_final: 0.7688 (t60) REVERT: C 511 ASN cc_start: 0.8360 (m-40) cc_final: 0.7955 (m-40) REVERT: C 521 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4021 (p90) REVERT: C 528 MET cc_start: 0.7433 (mpp) cc_final: 0.6907 (mmt) REVERT: D 141 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7266 (tp-100) REVERT: D 145 ASP cc_start: 0.6929 (m-30) cc_final: 0.6432 (m-30) REVERT: D 457 TRP cc_start: 0.7971 (t60) cc_final: 0.7689 (t60) REVERT: D 521 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.4239 (p-80) outliers start: 49 outliers final: 36 residues processed: 208 average time/residue: 0.2646 time to fit residues: 91.8971 Evaluate side-chains 202 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 191 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 464 TRP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20288 Z= 0.167 Angle : 0.557 9.485 27576 Z= 0.259 Chirality : 0.037 0.127 3144 Planarity : 0.003 0.055 3396 Dihedral : 4.740 52.959 2716 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.72 % Allowed : 17.50 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.07 (0.17), residues: 2452 helix: 1.43 (0.15), residues: 1396 sheet: 0.24 (0.64), residues: 72 loop : -2.12 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.003 0.001 HIS C 521 PHE 0.011 0.001 PHE B 705 TYR 0.011 0.001 TYR A 162 ARG 0.002 0.000 ARG B 706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 164 time to evaluate : 2.273 Fit side-chains REVERT: A 457 TRP cc_start: 0.7982 (t60) cc_final: 0.7698 (t60) REVERT: A 521 HIS cc_start: 0.5200 (OUTLIER) cc_final: 0.4367 (p-80) REVERT: B 141 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7455 (tp-100) REVERT: B 145 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: B 457 TRP cc_start: 0.7981 (t60) cc_final: 0.7692 (t60) REVERT: B 521 HIS cc_start: 0.5329 (OUTLIER) cc_final: 0.4284 (p-80) REVERT: C 457 TRP cc_start: 0.7982 (t60) cc_final: 0.7694 (t60) REVERT: C 521 HIS cc_start: 0.5370 (OUTLIER) cc_final: 0.4167 (p90) REVERT: C 528 MET cc_start: 0.7461 (mpp) cc_final: 0.6913 (mmt) REVERT: D 141 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7310 (tp-100) REVERT: D 145 ASP cc_start: 0.6963 (m-30) cc_final: 0.6494 (m-30) REVERT: D 457 TRP cc_start: 0.7960 (t60) cc_final: 0.7678 (t60) REVERT: D 521 HIS cc_start: 0.5268 (OUTLIER) cc_final: 0.4253 (p-80) outliers start: 57 outliers final: 38 residues processed: 207 average time/residue: 0.2503 time to fit residues: 86.8678 Evaluate side-chains 204 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 162 TYR Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 162 TYR Chi-restraints excluded: chain D residue 191 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 525 TYR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105381 restraints weight = 35180.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108076 restraints weight = 23081.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109844 restraints weight = 17485.110| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20288 Z= 0.338 Angle : 0.656 10.158 27576 Z= 0.310 Chirality : 0.040 0.211 3144 Planarity : 0.004 0.057 3396 Dihedral : 5.034 49.244 2716 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.29 % Allowed : 17.83 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.26 (0.17), residues: 2452 helix: 1.06 (0.14), residues: 1408 sheet: 0.14 (0.63), residues: 72 loop : -2.13 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 660 HIS 0.008 0.001 HIS D 169 PHE 0.016 0.002 PHE B 397 TYR 0.015 0.002 TYR A 162 ARG 0.002 0.000 ARG B 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.18 seconds wall clock time: 56 minutes 55.63 seconds (3415.63 seconds total)