Starting phenix.real_space_refine on Sun Feb 18 01:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekp_28209/02_2024/8ekp_28209_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 112 5.16 5 C 13368 2.51 5 N 3404 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20448 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5042 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.37, per 1000 atoms: 0.56 Number of scatterers: 20448 At special positions: 0 Unit cell: (137.97, 137.97, 112.42, 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 112 16.00 P 8 15.00 O 3556 8.00 N 3404 7.00 C 13368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.43 Conformation dependent library (CDL) restraints added in 4.0 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 55.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 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 134 through 145 Proline residue: A 138 - end of helix removed outlier: 3.870A pdb=" N GLN A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.529A pdb=" N VAL A 184 " --> pdb=" O VAL A 180 " (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 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 413 removed outlier: 5.217A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 467 through 491 removed outlier: 7.391A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 517 removed outlier: 3.757A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.748A pdb=" N VAL A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 503 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 508 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 510 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.683A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 removed outlier: 4.121A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 648 Processing helix chain 'A' and resid 656 through 673 removed outlier: 4.193A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.580A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 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 134 through 145 Proline residue: B 138 - end of helix removed outlier: 3.870A pdb=" N GLN B 141 " --> pdb=" O MET B 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.529A pdb=" N VAL B 184 " --> pdb=" O VAL B 180 " (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 261 through 281 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 378 through 413 removed outlier: 5.217A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 467 through 491 removed outlier: 7.391A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 517 removed outlier: 3.757A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.748A pdb=" N VAL B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 503 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 508 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 510 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.683A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 603 removed outlier: 4.121A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 648 Processing helix chain 'B' and resid 656 through 673 removed outlier: 4.193A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.580A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 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 134 through 145 Proline residue: C 138 - end of helix removed outlier: 3.870A pdb=" N GLN C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.529A pdb=" N VAL C 184 " --> pdb=" O VAL C 180 " (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 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 378 through 413 removed outlier: 5.217A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 467 through 491 removed outlier: 7.391A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 517 removed outlier: 3.757A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.748A pdb=" N VAL C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 503 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 508 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 510 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 534 through 558 removed outlier: 3.683A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 4.121A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 648 Processing helix chain 'C' and resid 656 through 673 removed outlier: 4.193A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.580A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 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 134 through 145 Proline residue: D 138 - end of helix removed outlier: 3.870A pdb=" N GLN D 141 " --> pdb=" O MET D 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.529A pdb=" N VAL D 184 " --> pdb=" O VAL D 180 " (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 261 through 281 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 378 through 413 removed outlier: 5.217A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 467 through 491 removed outlier: 7.391A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 517 removed outlier: 3.757A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.748A pdb=" N VAL D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 503 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 508 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 510 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 534 through 558 removed outlier: 3.683A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 557 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 603 removed outlier: 4.121A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 648 Processing helix chain 'D' and resid 656 through 673 removed outlier: 4.193A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.580A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 692 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A 702 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 690 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS A 704 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 688 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 692 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 692 " --> pdb=" O ASP C 700 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 702 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS C 690 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS C 704 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU C 688 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.986A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY D 692 " --> pdb=" O ASP D 700 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG D 702 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS D 690 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS D 704 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU D 688 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2520 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: 5.91 Time building geometry restraints manager: 9.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3160 1.31 - 1.43: 5844 1.43 - 1.56: 11736 1.56 - 1.69: 20 1.69 - 1.81: 172 Bond restraints: 20932 Sorted by residual: bond pdb=" C4 PEX D 802 " pdb=" O4 PEX D 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX C 802 " pdb=" O4 PEX C 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX B 802 " pdb=" O4 PEX B 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 802 " pdb=" O4 PEX A 802 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 20927 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 556 106.97 - 113.75: 11508 113.75 - 120.53: 8517 120.53 - 127.31: 7486 127.31 - 134.09: 245 Bond angle restraints: 28312 Sorted by residual: angle pdb=" O3 PEX A 802 " pdb=" P1 PEX A 802 " pdb=" O8 PEX A 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 802 " pdb=" P1 PEX B 802 " pdb=" O8 PEX B 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX C 802 " pdb=" P1 PEX C 802 " pdb=" O8 PEX C 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX D 802 " pdb=" P1 PEX D 802 " pdb=" O8 PEX D 802 " ideal model delta sigma weight residual 93.74 109.87 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.48 -15.74 3.00e+00 1.11e-01 2.75e+01 ... (remaining 28307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 12052 30.87 - 61.73: 360 61.73 - 92.60: 20 92.60 - 123.47: 0 123.47 - 154.33: 4 Dihedral angle restraints: 12436 sinusoidal: 5164 harmonic: 7272 Sorted by residual: dihedral pdb=" CA ARG A 539 " pdb=" C ARG A 539 " pdb=" N PHE A 540 " pdb=" CA PHE A 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG B 539 " pdb=" C ARG B 539 " pdb=" N PHE B 540 " pdb=" CA PHE B 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ARG C 539 " pdb=" C ARG C 539 " pdb=" N PHE C 540 " pdb=" CA PHE C 540 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 12433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2350 0.045 - 0.090: 646 0.090 - 0.134: 132 0.134 - 0.179: 12 0.179 - 0.224: 20 Chirality restraints: 3160 Sorted by residual: chirality pdb=" CG LEU B 636 " pdb=" CB LEU B 636 " pdb=" CD1 LEU B 636 " pdb=" CD2 LEU B 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU C 636 " pdb=" CB LEU C 636 " pdb=" CD1 LEU C 636 " pdb=" CD2 LEU C 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3157 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN B 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN B 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 530 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 530 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN C 530 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN C 530 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN C 530 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 530 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" CD GLN A 530 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN A 530 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 530 " -0.014 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5236 2.80 - 3.32: 18048 3.32 - 3.85: 34116 3.85 - 4.37: 41780 4.37 - 4.90: 69172 Nonbonded interactions: 168352 Sorted by model distance: nonbonded pdb=" O GLY D 131 " pdb=" OG SER D 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY A 131 " pdb=" OG SER A 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY B 131 " pdb=" OG SER B 176 " model vdw 2.269 2.440 nonbonded pdb=" O GLY C 131 " pdb=" OG SER C 176 " model vdw 2.269 2.440 nonbonded pdb=" O MET C 468 " pdb=" N1 PEX C 801 " model vdw 2.415 2.520 ... (remaining 168347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.680 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 56.670 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.004 0.075 20932 Z= 0.255 Angle : 0.874 16.126 28312 Z= 0.417 Chirality : 0.044 0.224 3160 Planarity : 0.007 0.093 3492 Dihedral : 14.700 154.331 7732 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.14), residues: 2448 helix: -2.37 (0.09), residues: 1424 sheet: 1.00 (0.52), residues: 112 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS C 251 PHE 0.014 0.001 PHE D 161 TYR 0.022 0.001 TYR B 544 ARG 0.017 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.384 Fit side-chains REVERT: A 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7085 (t0) REVERT: A 617 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6836 (ttm-80) REVERT: A 654 ASP cc_start: 0.6134 (t70) cc_final: 0.5786 (t70) REVERT: A 701 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 76 ASP cc_start: 0.7524 (t0) cc_final: 0.6384 (p0) REVERT: B 617 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: B 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5792 (t70) REVERT: B 701 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 76 ASP cc_start: 0.7525 (t0) cc_final: 0.7094 (t0) REVERT: C 617 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6830 (ttm-80) REVERT: C 654 ASP cc_start: 0.6129 (t70) cc_final: 0.5776 (t70) REVERT: C 701 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7397 (mt-10) REVERT: D 76 ASP cc_start: 0.7519 (t0) cc_final: 0.7087 (t0) REVERT: D 617 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6844 (ttm-80) REVERT: D 654 ASP cc_start: 0.6138 (t70) cc_final: 0.5788 (t70) REVERT: D 701 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7402 (mt-10) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 1.2183 time to fit residues: 526.3506 Evaluate side-chains 311 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 186 ASN A 234 HIS A 235 GLN A 354 ASN A 383 GLN A 487 GLN A 673 ASN B 165 HIS B 186 ASN B 235 GLN B 354 ASN B 383 GLN B 487 GLN B 673 ASN C 165 HIS C 186 ASN C 235 GLN C 354 ASN C 383 GLN C 487 GLN C 673 ASN D 165 HIS D 186 ASN D 234 HIS D 235 GLN D 354 ASN D 383 GLN D 487 GLN D 673 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 20932 Z= 0.488 Angle : 0.699 9.305 28312 Z= 0.352 Chirality : 0.047 0.159 3160 Planarity : 0.006 0.060 3492 Dihedral : 11.277 148.952 2960 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.15 % Allowed : 6.82 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2448 helix: -0.30 (0.13), residues: 1472 sheet: 1.16 (0.51), residues: 112 loop : -1.00 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 333 HIS 0.005 0.002 HIS B 165 PHE 0.028 0.002 PHE D 407 TYR 0.022 0.003 TYR B 515 ARG 0.005 0.001 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 355 time to evaluate : 2.373 Fit side-chains REVERT: A 76 ASP cc_start: 0.7581 (t0) cc_final: 0.7150 (t0) REVERT: A 645 MET cc_start: 0.8238 (mtm) cc_final: 0.8022 (mtm) REVERT: A 683 HIS cc_start: 0.7581 (t-90) cc_final: 0.7149 (t-90) REVERT: B 645 MET cc_start: 0.8231 (mtm) cc_final: 0.8025 (mtm) REVERT: B 683 HIS cc_start: 0.7582 (t-90) cc_final: 0.7146 (t-90) REVERT: C 645 MET cc_start: 0.8236 (mtm) cc_final: 0.8033 (mtm) REVERT: C 683 HIS cc_start: 0.7583 (t-90) cc_final: 0.7152 (t-90) REVERT: D 683 HIS cc_start: 0.7566 (t-90) cc_final: 0.7138 (t-90) outliers start: 47 outliers final: 20 residues processed: 372 average time/residue: 1.2315 time to fit residues: 523.7072 Evaluate side-chains 334 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 314 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 414 GLN A 452 GLN A 673 ASN B 186 ASN B 235 GLN B 414 GLN B 452 GLN B 673 ASN C 186 ASN C 235 GLN C 414 GLN C 452 GLN C 673 ASN D 186 ASN D 234 HIS D 235 GLN D 414 GLN D 673 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20932 Z= 0.169 Angle : 0.475 8.513 28312 Z= 0.245 Chirality : 0.038 0.174 3160 Planarity : 0.004 0.052 3492 Dihedral : 10.223 140.818 2960 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.20 % Allowed : 11.26 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2448 helix: 0.78 (0.14), residues: 1472 sheet: 1.39 (0.52), residues: 112 loop : -0.87 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.002 0.001 HIS D 251 PHE 0.014 0.001 PHE B 540 TYR 0.016 0.001 TYR D 525 ARG 0.005 0.000 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 2.406 Fit side-chains REVERT: A 76 ASP cc_start: 0.7558 (t0) cc_final: 0.7135 (t0) REVERT: A 503 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7828 (tp) REVERT: A 647 GLU cc_start: 0.7537 (tt0) cc_final: 0.7021 (pt0) REVERT: B 76 ASP cc_start: 0.7534 (t0) cc_final: 0.7186 (t0) REVERT: B 503 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7819 (tp) REVERT: B 647 GLU cc_start: 0.7532 (tt0) cc_final: 0.7019 (pt0) REVERT: C 76 ASP cc_start: 0.7540 (t0) cc_final: 0.7190 (t0) REVERT: C 182 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7801 (tt) REVERT: C 503 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 647 GLU cc_start: 0.7547 (tt0) cc_final: 0.7022 (pt0) REVERT: D 76 ASP cc_start: 0.7554 (t0) cc_final: 0.7211 (t0) REVERT: D 182 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7784 (tt) REVERT: D 234 HIS cc_start: 0.7458 (m-70) cc_final: 0.7140 (m170) REVERT: D 503 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7819 (tp) REVERT: D 647 GLU cc_start: 0.7533 (tt0) cc_final: 0.7022 (pt0) outliers start: 48 outliers final: 24 residues processed: 349 average time/residue: 1.2251 time to fit residues: 487.6962 Evaluate side-chains 342 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 312 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN B 186 ASN B 673 ASN C 186 ASN C 673 ASN D 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20932 Z= 0.277 Angle : 0.544 9.471 28312 Z= 0.275 Chirality : 0.041 0.182 3160 Planarity : 0.004 0.051 3492 Dihedral : 10.322 141.460 2960 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.47 % Allowed : 13.05 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2448 helix: 0.91 (0.14), residues: 1480 sheet: 1.61 (0.60), residues: 88 loop : -0.82 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 333 HIS 0.004 0.001 HIS D 251 PHE 0.016 0.002 PHE C 405 TYR 0.014 0.002 TYR B 525 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 311 time to evaluate : 2.429 Fit side-chains REVERT: A 76 ASP cc_start: 0.7560 (t0) cc_final: 0.7138 (t0) REVERT: A 503 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7843 (tp) REVERT: A 512 LEU cc_start: 0.8926 (mt) cc_final: 0.8719 (mm) REVERT: B 503 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (tp) REVERT: D 234 HIS cc_start: 0.7464 (m-70) cc_final: 0.7208 (m170) REVERT: D 503 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7831 (tp) outliers start: 54 outliers final: 33 residues processed: 343 average time/residue: 1.1668 time to fit residues: 459.9806 Evaluate side-chains 327 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 291 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 0.0000 chunk 215 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 673 ASN B 186 ASN B 235 GLN B 414 GLN B 673 ASN C 186 ASN C 235 GLN C 673 ASN D 186 ASN D 235 GLN D 414 GLN D 452 GLN D 673 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20932 Z= 0.132 Angle : 0.460 9.623 28312 Z= 0.232 Chirality : 0.037 0.184 3160 Planarity : 0.003 0.045 3492 Dihedral : 9.813 134.915 2960 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.20 % Allowed : 13.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2448 helix: 1.31 (0.14), residues: 1464 sheet: 1.96 (0.61), residues: 88 loop : -0.67 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.002 0.001 HIS C 251 PHE 0.021 0.001 PHE C 540 TYR 0.014 0.001 TYR D 525 ARG 0.006 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 313 time to evaluate : 2.365 Fit side-chains REVERT: A 76 ASP cc_start: 0.7597 (t0) cc_final: 0.7185 (t0) REVERT: A 503 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 182 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 503 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7756 (tp) REVERT: C 182 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 503 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7756 (tp) REVERT: D 234 HIS cc_start: 0.7399 (m-70) cc_final: 0.7086 (m170) REVERT: D 503 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7754 (tp) outliers start: 48 outliers final: 21 residues processed: 344 average time/residue: 1.2216 time to fit residues: 479.6094 Evaluate side-chains 328 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 301 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN B 186 ASN B 235 GLN C 186 ASN C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20932 Z= 0.259 Angle : 0.531 9.750 28312 Z= 0.266 Chirality : 0.041 0.199 3160 Planarity : 0.004 0.046 3492 Dihedral : 10.033 133.930 2960 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.52 % Allowed : 14.70 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2448 helix: 1.21 (0.14), residues: 1460 sheet: 1.88 (0.60), residues: 88 loop : -0.69 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 333 HIS 0.004 0.001 HIS D 251 PHE 0.018 0.002 PHE B 405 TYR 0.014 0.002 TYR D 525 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 319 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 503 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 182 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 234 HIS cc_start: 0.7409 (m-70) cc_final: 0.7175 (m170) REVERT: B 503 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 182 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7813 (tt) REVERT: C 503 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7825 (tp) REVERT: D 182 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7825 (tt) REVERT: D 234 HIS cc_start: 0.7443 (m-70) cc_final: 0.7131 (m170) REVERT: D 503 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7823 (tp) outliers start: 55 outliers final: 35 residues processed: 364 average time/residue: 1.2126 time to fit residues: 503.9801 Evaluate side-chains 350 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 307 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 0.1980 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 673 ASN B 186 ASN B 414 GLN C 186 ASN C 673 ASN D 186 ASN D 414 GLN D 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20932 Z= 0.194 Angle : 0.497 10.332 28312 Z= 0.249 Chirality : 0.039 0.214 3160 Planarity : 0.003 0.044 3492 Dihedral : 9.794 128.571 2960 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.79 % Allowed : 14.19 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2448 helix: 1.31 (0.14), residues: 1468 sheet: 1.93 (0.61), residues: 88 loop : -0.63 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 333 HIS 0.003 0.001 HIS C 251 PHE 0.018 0.001 PHE D 405 TYR 0.014 0.001 TYR A 525 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 503 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 503 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 645 MET cc_start: 0.7915 (ttm) cc_final: 0.7673 (mtp) REVERT: C 182 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7832 (tt) REVERT: C 234 HIS cc_start: 0.7398 (m-70) cc_final: 0.7102 (m170) REVERT: C 503 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7811 (tp) REVERT: D 182 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (tt) REVERT: D 234 HIS cc_start: 0.7430 (m-70) cc_final: 0.7083 (m170) REVERT: D 503 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7811 (tp) outliers start: 61 outliers final: 44 residues processed: 367 average time/residue: 1.1790 time to fit residues: 497.6663 Evaluate side-chains 363 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 312 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 235 GLN C 673 ASN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20932 Z= 0.225 Angle : 0.524 10.259 28312 Z= 0.261 Chirality : 0.040 0.215 3160 Planarity : 0.004 0.043 3492 Dihedral : 9.778 123.832 2960 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.52 % Allowed : 14.84 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2448 helix: 1.29 (0.14), residues: 1468 sheet: 1.91 (0.60), residues: 88 loop : -0.63 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 333 HIS 0.003 0.001 HIS D 251 PHE 0.019 0.001 PHE C 540 TYR 0.013 0.002 TYR D 525 ARG 0.006 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 319 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7813 (tt) REVERT: A 503 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7819 (tp) REVERT: B 182 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 503 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 645 MET cc_start: 0.7943 (mtm) cc_final: 0.7717 (mtp) REVERT: C 182 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7842 (tt) REVERT: C 234 HIS cc_start: 0.7436 (m-70) cc_final: 0.7139 (m170) REVERT: C 503 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7815 (tp) REVERT: D 182 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7843 (tt) REVERT: D 234 HIS cc_start: 0.7445 (m-70) cc_final: 0.7103 (m170) REVERT: D 503 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7821 (tp) REVERT: D 647 GLU cc_start: 0.7427 (tt0) cc_final: 0.6978 (mp0) outliers start: 55 outliers final: 39 residues processed: 362 average time/residue: 1.2355 time to fit residues: 510.2178 Evaluate side-chains 359 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 312 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 492 MET Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.0770 chunk 208 optimal weight: 0.0970 chunk 222 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 201 optimal weight: 0.1980 chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 234 HIS A 673 ASN B 186 ASN B 673 ASN C 186 ASN C 673 ASN D 186 ASN D 235 GLN D 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20932 Z= 0.112 Angle : 0.460 9.434 28312 Z= 0.229 Chirality : 0.036 0.189 3160 Planarity : 0.003 0.041 3492 Dihedral : 8.893 113.113 2960 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.70 % Allowed : 15.06 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2448 helix: 1.61 (0.14), residues: 1452 sheet: 2.12 (0.62), residues: 88 loop : -0.60 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 657 HIS 0.002 0.001 HIS B 438 PHE 0.019 0.001 PHE D 540 TYR 0.012 0.001 TYR C 525 ARG 0.006 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 447 TYR cc_start: 0.8397 (t80) cc_final: 0.8187 (t80) REVERT: A 503 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7401 (mp) REVERT: A 647 GLU cc_start: 0.7417 (tt0) cc_final: 0.6973 (mp0) REVERT: B 372 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8243 (mtm) REVERT: B 447 TYR cc_start: 0.8391 (t80) cc_final: 0.8183 (t80) REVERT: B 647 GLU cc_start: 0.7473 (tt0) cc_final: 0.7000 (mp0) REVERT: C 289 GLU cc_start: 0.7943 (mp0) cc_final: 0.7599 (mp0) REVERT: C 372 MET cc_start: 0.8671 (mtp) cc_final: 0.8341 (mtm) REVERT: C 503 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 647 GLU cc_start: 0.7392 (tt0) cc_final: 0.6966 (mp0) REVERT: D 182 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7843 (tt) REVERT: D 372 MET cc_start: 0.8683 (mtp) cc_final: 0.8349 (mtm) REVERT: D 503 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7361 (mp) REVERT: D 647 GLU cc_start: 0.7370 (tt0) cc_final: 0.6906 (mp0) outliers start: 59 outliers final: 29 residues processed: 382 average time/residue: 1.2584 time to fit residues: 546.8608 Evaluate side-chains 357 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 322 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 235 GLN A 673 ASN B 186 ASN B 235 GLN B 673 ASN C 186 ASN C 235 GLN D 186 ASN D 235 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20932 Z= 0.264 Angle : 0.560 10.040 28312 Z= 0.274 Chirality : 0.041 0.248 3160 Planarity : 0.004 0.043 3492 Dihedral : 9.513 117.355 2960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 16.35 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2448 helix: 1.38 (0.14), residues: 1460 sheet: 1.92 (0.61), residues: 88 loop : -0.61 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS D 202 PHE 0.021 0.002 PHE A 405 TYR 0.018 0.002 TYR D 447 ARG 0.006 0.000 ARG D 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 2.551 Fit side-chains REVERT: A 182 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 503 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7821 (tp) REVERT: A 535 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5973 (pmt-80) REVERT: B 372 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8624 (mtm) REVERT: B 503 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 535 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5976 (pmt-80) REVERT: C 234 HIS cc_start: 0.7473 (m-70) cc_final: 0.7178 (m170) REVERT: C 503 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7818 (tp) REVERT: C 535 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5976 (pmt-80) REVERT: C 647 GLU cc_start: 0.7479 (tt0) cc_final: 0.7049 (mp0) REVERT: D 182 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7836 (tt) REVERT: D 234 HIS cc_start: 0.7457 (m-70) cc_final: 0.7114 (m170) REVERT: D 503 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7819 (tp) REVERT: D 535 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5972 (pmt-80) outliers start: 44 outliers final: 23 residues processed: 354 average time/residue: 1.2096 time to fit residues: 490.2325 Evaluate side-chains 345 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 311 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 673 ASN B 186 ASN B 673 ASN C 186 ASN C 673 ASN D 186 ASN D 673 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114664 restraints weight = 23552.965| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.56 r_work: 0.3103 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20932 Z= 0.254 Angle : 0.553 10.152 28312 Z= 0.272 Chirality : 0.040 0.247 3160 Planarity : 0.004 0.044 3492 Dihedral : 9.516 117.425 2960 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 16.44 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2448 helix: 1.31 (0.14), residues: 1468 sheet: 1.95 (0.60), residues: 88 loop : -0.61 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 333 HIS 0.003 0.001 HIS D 251 PHE 0.019 0.002 PHE A 405 TYR 0.020 0.002 TYR C 447 ARG 0.006 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7892.59 seconds wall clock time: 140 minutes 58.39 seconds (8458.39 seconds total)