Starting phenix.real_space_refine on Sat May 18 06:27:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1d_35919/05_2024/8j1d_35919.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 13132 2.51 5 N 3340 2.21 5 O 3620 1.98 5 H 20492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 40688 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "B" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "C" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Chain: "D" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10172 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 1 Time building chain proxies: 17.10, per 1000 atoms: 0.42 Number of scatterers: 40688 At special positions: 0 Unit cell: (157.17, 157.17, 126.48, 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 104 16.00 O 3620 8.00 N 3340 7.00 C 13132 6.00 H 20492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.04 Conformation dependent library (CDL) restraints added in 3.8 seconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 63.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.911A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.445A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.541A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 4.024A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.700A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.586A pdb=" N ASN A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.740A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.579A pdb=" N MET A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.840A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 725 Processing helix chain 'A' and resid 726 through 748 removed outlier: 3.670A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.561A pdb=" N GLY A 765 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.939A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.453A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.510A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 4.024A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.700A pdb=" N GLN B 274 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 357 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.584A pdb=" N ASN B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 491 Processing helix chain 'B' and resid 504 through 534 Processing helix chain 'B' and resid 549 through 570 Processing helix chain 'B' and resid 575 through 592 removed outlier: 3.701A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 589 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 removed outlier: 3.593A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.844A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 681 removed outlier: 3.778A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 725 Processing helix chain 'B' and resid 726 through 748 removed outlier: 3.671A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.564A pdb=" N GLY B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.938A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.448A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.537A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 4.023A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.698A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 336 through 357 Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.585A pdb=" N ASN C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 453 through 464 Processing helix chain 'C' and resid 468 through 491 Processing helix chain 'C' and resid 504 through 534 Processing helix chain 'C' and resid 549 through 570 Processing helix chain 'C' and resid 575 through 592 removed outlier: 3.734A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 589 " --> pdb=" O GLY C 585 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.577A pdb=" N MET C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 637 removed outlier: 3.844A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 725 Processing helix chain 'C' and resid 726 through 748 removed outlier: 3.670A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.562A pdb=" N GLY C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.927A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.448A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.537A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 4.022A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.698A pdb=" N GLN D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 336 through 357 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.585A pdb=" N ASN D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 504 through 534 Processing helix chain 'D' and resid 549 through 570 Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.748A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 589 " --> pdb=" O GLY D 585 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.579A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 637 removed outlier: 3.845A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 681 removed outlier: 3.777A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 725 Processing helix chain 'D' and resid 726 through 748 removed outlier: 3.671A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.562A pdb=" N GLY D 765 " --> pdb=" O VAL D 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.056A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.062A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.057A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.056A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3156 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: 17.35 Time building geometry restraints manager: 32.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20452 1.03 - 1.22: 40 1.22 - 1.42: 8654 1.42 - 1.61: 11838 1.61 - 1.81: 168 Bond restraints: 41152 Sorted by residual: bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.24e+00 bond pdb=" N VAL C 148 " pdb=" H VAL C 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.22e+00 bond pdb=" N VAL B 148 " pdb=" H VAL B 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" N VAL A 148 " pdb=" H VAL A 148 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 41147 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.61: 334 105.61 - 112.73: 47832 112.73 - 119.84: 10954 119.84 - 126.96: 15050 126.96 - 134.08: 218 Bond angle restraints: 74388 Sorted by residual: angle pdb=" C SER A 650 " pdb=" N ASN A 651 " pdb=" CA ASN A 651 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C SER D 650 " pdb=" N ASN D 651 " pdb=" CA ASN D 651 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C SER C 650 " pdb=" N ASN C 651 " pdb=" CA ASN C 651 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 angle pdb=" C SER B 650 " pdb=" N ASN B 651 " pdb=" CA ASN B 651 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.58e+00 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 108.76 3.24 1.40e+00 5.10e-01 5.37e+00 ... (remaining 74383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 17012 16.42 - 32.83: 1649 32.83 - 49.25: 494 49.25 - 65.66: 157 65.66 - 82.08: 28 Dihedral angle restraints: 19340 sinusoidal: 10400 harmonic: 8940 Sorted by residual: dihedral pdb=" CG ARG B 404 " pdb=" CD ARG B 404 " pdb=" NE ARG B 404 " pdb=" CZ ARG B 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.63 -42.37 2 1.50e+01 4.44e-03 9.69e+00 dihedral pdb=" CG ARG C 404 " pdb=" CD ARG C 404 " pdb=" NE ARG C 404 " pdb=" CZ ARG C 404 " ideal model delta sinusoidal sigma weight residual 180.00 -137.64 -42.36 2 1.50e+01 4.44e-03 9.69e+00 dihedral pdb=" CG ARG D 404 " pdb=" CD ARG D 404 " pdb=" NE ARG D 404 " pdb=" CZ ARG D 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.65 -42.35 2 1.50e+01 4.44e-03 9.68e+00 ... (remaining 19337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2189 0.033 - 0.065: 802 0.065 - 0.098: 190 0.098 - 0.130: 38 0.130 - 0.163: 5 Chirality restraints: 3224 Sorted by residual: chirality pdb=" CB THR D 701 " pdb=" CA THR D 701 " pdb=" OG1 THR D 701 " pdb=" CG2 THR D 701 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB THR A 701 " pdb=" CA THR A 701 " pdb=" OG1 THR A 701 " pdb=" CG2 THR A 701 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB THR C 701 " pdb=" CA THR C 701 " pdb=" OG1 THR C 701 " pdb=" CG2 THR C 701 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3221 not shown) Planarity restraints: 5912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 583 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C VAL B 583 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL B 583 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 584 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 498 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 499 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 498 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 499 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.030 5.00e-02 4.00e+02 ... (remaining 5909 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3408 2.20 - 2.80: 85239 2.80 - 3.40: 113717 3.40 - 4.00: 140040 4.00 - 4.60: 218975 Nonbonded interactions: 561379 Sorted by model distance: nonbonded pdb=" O ILE C 744 " pdb=" HG SER C 747 " model vdw 1.599 1.850 nonbonded pdb=" O ILE D 744 " pdb=" HG SER D 747 " model vdw 1.600 1.850 nonbonded pdb=" O ILE A 744 " pdb=" HG SER A 747 " model vdw 1.601 1.850 nonbonded pdb=" O ILE B 744 " pdb=" HG SER B 747 " model vdw 1.601 1.850 nonbonded pdb=" O SER A 726 " pdb=" H SER A 729 " model vdw 1.608 1.850 ... (remaining 561374 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.130 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: 0.620 Extract box with map and model: 7.800 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 123.160 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.180 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 : 0.003 0.070 20660 Z= 0.184 Angle : 0.594 6.768 28020 Z= 0.322 Chirality : 0.035 0.163 3224 Planarity : 0.004 0.054 3500 Dihedral : 14.255 80.426 7532 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.36 % Favored : 89.72 % Rotamer: Outliers : 0.09 % Allowed : 11.13 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2500 helix: 0.34 (0.14), residues: 1464 sheet: 0.06 (0.70), residues: 56 loop : -2.54 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 409 HIS 0.006 0.001 HIS A 731 PHE 0.016 0.001 PHE B 707 TYR 0.010 0.001 TYR B 556 ARG 0.002 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.7025 time to fit residues: 167.9014 Evaluate side-chains 147 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20660 Z= 0.496 Angle : 0.705 7.810 28020 Z= 0.385 Chirality : 0.040 0.135 3224 Planarity : 0.006 0.060 3500 Dihedral : 4.998 41.011 2770 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.96 % Allowed : 13.88 % Favored : 85.16 % Rotamer: Outliers : 1.97 % Allowed : 12.07 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2500 helix: -0.14 (0.13), residues: 1492 sheet: -0.24 (0.67), residues: 56 loop : -2.90 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 409 HIS 0.007 0.001 HIS C 388 PHE 0.024 0.002 PHE D 341 TYR 0.016 0.002 TYR D 556 ARG 0.008 0.001 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 TYR cc_start: 0.5498 (OUTLIER) cc_final: 0.4913 (m-10) REVERT: B 628 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4905 (m-10) REVERT: D 628 TYR cc_start: 0.5531 (OUTLIER) cc_final: 0.4980 (m-10) outliers start: 44 outliers final: 33 residues processed: 180 average time/residue: 0.6680 time to fit residues: 192.1970 Evaluate side-chains 175 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20660 Z= 0.231 Angle : 0.568 6.363 28020 Z= 0.303 Chirality : 0.035 0.122 3224 Planarity : 0.005 0.059 3500 Dihedral : 4.556 42.544 2770 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.04 % Favored : 89.00 % Rotamer: Outliers : 1.62 % Allowed : 12.84 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2500 helix: 0.32 (0.13), residues: 1488 sheet: -0.20 (0.67), residues: 56 loop : -2.63 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 409 HIS 0.004 0.001 HIS A 388 PHE 0.023 0.001 PHE D 466 TYR 0.009 0.001 TYR D 702 ARG 0.004 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8280 (pt) REVERT: A 628 TYR cc_start: 0.5259 (OUTLIER) cc_final: 0.4841 (m-10) REVERT: B 331 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (pt) REVERT: B 578 MET cc_start: 0.5539 (tpt) cc_final: 0.5310 (tpt) REVERT: B 628 TYR cc_start: 0.5256 (OUTLIER) cc_final: 0.4834 (m-10) outliers start: 36 outliers final: 25 residues processed: 164 average time/residue: 0.6955 time to fit residues: 181.4089 Evaluate side-chains 163 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN C 445 ASN D 445 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20660 Z= 0.358 Angle : 0.617 7.472 28020 Z= 0.331 Chirality : 0.037 0.127 3224 Planarity : 0.005 0.062 3500 Dihedral : 4.715 45.215 2770 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.96 % Allowed : 12.80 % Favored : 86.24 % Rotamer: Outliers : 2.06 % Allowed : 13.60 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2500 helix: 0.21 (0.13), residues: 1488 sheet: -0.22 (0.67), residues: 56 loop : -2.80 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 409 HIS 0.005 0.001 HIS C 388 PHE 0.021 0.002 PHE A 466 TYR 0.013 0.002 TYR B 556 ARG 0.004 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8400 (pt) REVERT: A 578 MET cc_start: 0.5592 (tpt) cc_final: 0.5375 (tpt) REVERT: A 628 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.4668 (m-10) REVERT: B 331 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (pt) REVERT: B 628 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.4662 (m-10) REVERT: C 331 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8334 (pt) REVERT: D 331 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8319 (pt) REVERT: D 578 MET cc_start: 0.5576 (tpt) cc_final: 0.5356 (tpt) outliers start: 46 outliers final: 39 residues processed: 173 average time/residue: 0.6857 time to fit residues: 189.3948 Evaluate side-chains 182 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20660 Z= 0.336 Angle : 0.605 7.295 28020 Z= 0.324 Chirality : 0.036 0.130 3224 Planarity : 0.005 0.062 3500 Dihedral : 4.741 46.457 2770 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.68 % Favored : 87.36 % Rotamer: Outliers : 2.42 % Allowed : 14.59 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2500 helix: 0.25 (0.13), residues: 1496 sheet: -0.29 (0.67), residues: 56 loop : -2.82 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 409 HIS 0.005 0.001 HIS D 388 PHE 0.029 0.002 PHE C 466 TYR 0.013 0.002 TYR B 556 ARG 0.004 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8314 (pt) REVERT: A 628 TYR cc_start: 0.5325 (OUTLIER) cc_final: 0.4685 (m-10) REVERT: B 331 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (pt) REVERT: B 628 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4659 (m-10) REVERT: C 331 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (pt) REVERT: C 574 TYR cc_start: 0.4134 (m-10) cc_final: 0.3899 (m-80) REVERT: D 331 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (pt) REVERT: D 574 TYR cc_start: 0.4073 (m-10) cc_final: 0.3850 (m-80) REVERT: D 628 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.4757 (m-10) outliers start: 54 outliers final: 36 residues processed: 180 average time/residue: 0.6800 time to fit residues: 196.0435 Evaluate side-chains 175 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20660 Z= 0.185 Angle : 0.538 6.037 28020 Z= 0.282 Chirality : 0.034 0.135 3224 Planarity : 0.004 0.059 3500 Dihedral : 4.362 46.630 2770 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.48 % Favored : 88.56 % Rotamer: Outliers : 1.44 % Allowed : 15.57 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2500 helix: 0.67 (0.13), residues: 1516 sheet: 0.12 (0.70), residues: 56 loop : -2.53 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.004 0.001 HIS A 309 PHE 0.018 0.001 PHE B 756 TYR 0.008 0.001 TYR D 502 ARG 0.002 0.000 ARG D 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 TYR cc_start: 0.5150 (OUTLIER) cc_final: 0.4591 (m-10) REVERT: B 628 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4663 (m-10) REVERT: C 331 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8298 (pt) REVERT: D 331 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8281 (pt) outliers start: 32 outliers final: 21 residues processed: 167 average time/residue: 0.7024 time to fit residues: 187.0189 Evaluate side-chains 161 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 776 TRP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 602 TYR Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 776 TRP Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 602 TYR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 776 TRP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 602 TYR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 776 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1657 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: