Starting phenix.real_space_refine on Thu Mar 14 19:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/03_2024/6p49_20247.pdb" } resolution = 3.3 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= 0.002 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 Ca 2 9.91 5 S 66 5.16 5 C 6352 2.51 5 N 1520 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 810": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4787 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4787 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.55 Number of scatterers: 9576 At special positions: 0 Unit cell: (84.72, 111.195, 106.959, 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) Ca 2 19.99 S 66 16.00 O 1636 8.00 N 1520 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.05 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.01 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=1.84 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.01 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=1.84 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: 3.36 Conformation dependent library (CDL) restraints added in 1.5 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 55.4% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.724A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.724A pdb=" N TYR A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.573A pdb=" N TYR A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 284 through 292 removed outlier: 4.026A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 327 removed outlier: 3.618A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 378 through 408 removed outlier: 3.871A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.767A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.558A pdb=" N SER A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 529 removed outlier: 3.824A pdb=" N SER A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.937A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 4.377A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.835A pdb=" N GLY A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 4.478A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 4.064A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 4.171A pdb=" N LEU A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 removed outlier: 3.617A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 removed outlier: 3.587A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.724A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.724A pdb=" N TYR B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.573A pdb=" N TYR B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.026A pdb=" N ILE B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 327 removed outlier: 3.617A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 378 through 408 removed outlier: 3.871A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.767A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.558A pdb=" N SER B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 529 removed outlier: 3.824A pdb=" N SER B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 547 through 563 removed outlier: 3.937A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 4.377A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 627 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.834A pdb=" N GLY B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.479A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 4.063A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 4.171A pdb=" N LEU B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.617A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 839 removed outlier: 3.586A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 837 " --> pdb=" O ALA B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 845 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.770A pdb=" N SER A 782 " --> pdb=" O TYR A 809 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.770A pdb=" N SER B 782 " --> pdb=" O TYR B 809 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1062 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: 2.32 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2795 1.34 - 1.46: 2362 1.46 - 1.58: 4581 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 9842 Sorted by residual: bond pdb=" C THR B 504 " pdb=" N PRO B 505 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.22e+00 bond pdb=" C THR A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.03e+00 bond pdb=" C PRO A 763 " pdb=" N PRO A 764 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.68e+00 bond pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.56e+00 bond pdb=" N PRO A 686 " pdb=" CD PRO A 686 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.31e+00 ... (remaining 9837 not shown) Histogram of bond angle deviations from ideal: 98.21 - 106.05: 302 106.05 - 113.89: 5222 113.89 - 121.73: 5973 121.73 - 129.57: 1771 129.57 - 137.41: 92 Bond angle restraints: 13360 Sorted by residual: angle pdb=" N VAL B 682 " pdb=" CA VAL B 682 " pdb=" C VAL B 682 " ideal model delta sigma weight residual 106.21 120.75 -14.54 1.07e+00 8.73e-01 1.85e+02 angle pdb=" N VAL A 682 " pdb=" CA VAL A 682 " pdb=" C VAL A 682 " ideal model delta sigma weight residual 106.21 120.74 -14.53 1.07e+00 8.73e-01 1.84e+02 angle pdb=" N GLN B 720 " pdb=" CA GLN B 720 " pdb=" C GLN B 720 " ideal model delta sigma weight residual 111.14 124.92 -13.78 1.08e+00 8.57e-01 1.63e+02 angle pdb=" N GLN A 720 " pdb=" CA GLN A 720 " pdb=" C GLN A 720 " ideal model delta sigma weight residual 111.14 124.88 -13.74 1.08e+00 8.57e-01 1.62e+02 angle pdb=" N ARG A 478 " pdb=" CA ARG A 478 " pdb=" C ARG A 478 " ideal model delta sigma weight residual 113.43 98.21 15.22 1.26e+00 6.30e-01 1.46e+02 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4989 17.97 - 35.95: 607 35.95 - 53.92: 122 53.92 - 71.89: 22 71.89 - 89.87: 12 Dihedral angle restraints: 5752 sinusoidal: 2312 harmonic: 3440 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual -86.00 -163.44 77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual -86.00 -163.38 77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual -86.00 -149.79 63.79 1 1.00e+01 1.00e-02 5.36e+01 ... (remaining 5749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1339 0.122 - 0.243: 114 0.243 - 0.364: 17 0.364 - 0.486: 8 0.486 - 0.607: 2 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CB VAL B 640 " pdb=" CA VAL B 640 " pdb=" CG1 VAL B 640 " pdb=" CG2 VAL B 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA ASP B 749 " pdb=" N ASP B 749 " pdb=" C ASP B 749 " pdb=" CB ASP B 749 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 1477 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA A 719 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN A 720 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 719 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ALA B 719 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA B 719 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN B 720 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 688 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 689 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 689 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 689 " 0.056 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 610 2.71 - 3.26: 9308 3.26 - 3.81: 15541 3.81 - 4.35: 19408 4.35 - 4.90: 30570 Nonbonded interactions: 75437 Sorted by model distance: nonbonded pdb=" O PRO B 628 " pdb=" O TRP B 629 " model vdw 2.164 3.040 nonbonded pdb=" O PRO A 628 " pdb=" O TRP A 629 " model vdw 2.164 3.040 nonbonded pdb=" CD1 TRP A 359 " pdb=" N ARG A 360 " model vdw 2.191 3.340 nonbonded pdb=" CD1 TRP B 359 " pdb=" N ARG B 360 " model vdw 2.191 3.340 nonbonded pdb=" OH TYR A 847 " pdb=" OH TYR B 847 " model vdw 2.221 2.440 ... (remaining 75432 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.790 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.380 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.007 0.067 9842 Z= 0.445 Angle : 1.501 15.220 13360 Z= 0.932 Chirality : 0.082 0.607 1480 Planarity : 0.010 0.101 1630 Dihedral : 16.183 89.867 3516 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.90 % Favored : 92.39 % Rotamer: Outliers : 3.28 % Allowed : 10.23 % Favored : 86.49 % 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: -6.27 (0.17), residues: 1130 helix: -4.42 (0.10), residues: 654 sheet: None (None), residues: 0 loop : -3.58 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 302 HIS 0.006 0.002 HIS B 275 PHE 0.030 0.003 PHE A 685 TYR 0.030 0.003 TYR A 306 ARG 0.006 0.001 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.5982 (mmm) cc_final: 0.5635 (mmt) REVERT: A 590 LYS cc_start: 0.4027 (OUTLIER) cc_final: 0.2743 (mmtt) REVERT: A 725 TRP cc_start: 0.6509 (m100) cc_final: 0.6083 (m100) REVERT: B 142 MET cc_start: 0.3547 (tpt) cc_final: 0.3199 (tpp) REVERT: B 553 MET cc_start: 0.5506 (mmm) cc_final: 0.5264 (mmt) REVERT: B 641 SER cc_start: 0.4003 (OUTLIER) cc_final: 0.3650 (t) outliers start: 34 outliers final: 10 residues processed: 222 average time/residue: 0.2412 time to fit residues: 71.8417 Evaluate side-chains 138 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 351 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 730 GLN A 740 ASN A 814 ASN A 825 ASN B 275 HIS B 351 GLN B 620 ASN B 621 ASN B 696 ASN B 730 GLN B 740 ASN B 814 ASN B 830 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9842 Z= 0.243 Angle : 0.825 12.218 13360 Z= 0.425 Chirality : 0.047 0.191 1480 Planarity : 0.007 0.066 1630 Dihedral : 8.307 50.395 1300 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.12 % Favored : 90.71 % Rotamer: Outliers : 3.38 % Allowed : 17.47 % Favored : 79.15 % 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: -5.21 (0.19), residues: 1130 helix: -3.16 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -3.82 (0.21), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 397 HIS 0.003 0.001 HIS A 824 PHE 0.016 0.002 PHE A 556 TYR 0.019 0.002 TYR B 847 ARG 0.010 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4211 (OUTLIER) cc_final: 0.2691 (mmtt) REVERT: A 598 PRO cc_start: 0.6767 (Cg_endo) cc_final: 0.6555 (Cg_exo) REVERT: A 601 CYS cc_start: 0.5805 (OUTLIER) cc_final: 0.5339 (m) REVERT: B 465 LEU cc_start: 0.8243 (tt) cc_final: 0.8025 (tt) REVERT: B 601 CYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5969 (m) REVERT: B 641 SER cc_start: 0.3647 (OUTLIER) cc_final: 0.3199 (t) REVERT: B 764 PRO cc_start: 0.6405 (Cg_endo) cc_final: 0.6067 (Cg_exo) outliers start: 35 outliers final: 16 residues processed: 183 average time/residue: 0.1892 time to fit residues: 49.4067 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 845 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS B 351 GLN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9842 Z= 0.204 Angle : 0.747 15.618 13360 Z= 0.380 Chirality : 0.045 0.199 1480 Planarity : 0.006 0.062 1630 Dihedral : 7.095 41.168 1289 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.27 % Favored : 89.56 % Rotamer: Outliers : 2.80 % Allowed : 20.37 % Favored : 76.83 % 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: -4.68 (0.20), residues: 1130 helix: -2.65 (0.17), residues: 642 sheet: None (None), residues: 0 loop : -3.71 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 302 HIS 0.005 0.001 HIS A 824 PHE 0.023 0.002 PHE A 556 TYR 0.020 0.002 TYR A 306 ARG 0.004 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4390 (OUTLIER) cc_final: 0.3049 (mmtt) outliers start: 29 outliers final: 19 residues processed: 161 average time/residue: 0.1794 time to fit residues: 42.3317 Evaluate side-chains 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9842 Z= 0.206 Angle : 0.726 13.012 13360 Z= 0.369 Chirality : 0.045 0.173 1480 Planarity : 0.005 0.061 1630 Dihedral : 6.743 39.664 1288 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.56 % Favored : 90.27 % Rotamer: Outliers : 3.57 % Allowed : 21.04 % Favored : 75.39 % 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: -4.39 (0.21), residues: 1130 helix: -2.42 (0.17), residues: 652 sheet: None (None), residues: 0 loop : -3.58 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 302 HIS 0.004 0.001 HIS B 824 PHE 0.025 0.002 PHE A 681 TYR 0.020 0.002 TYR A 306 ARG 0.003 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7760 (m) REVERT: A 590 LYS cc_start: 0.4505 (OUTLIER) cc_final: 0.3271 (mmtt) REVERT: B 478 ARG cc_start: 0.5894 (mtt90) cc_final: 0.5575 (mpt-90) REVERT: B 524 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7477 (tp) REVERT: B 725 TRP cc_start: 0.6400 (m100) cc_final: 0.6066 (m100) REVERT: B 764 PRO cc_start: 0.6694 (Cg_endo) cc_final: 0.6355 (Cg_exo) REVERT: B 773 MET cc_start: 0.5732 (mmm) cc_final: 0.5485 (mmm) outliers start: 37 outliers final: 26 residues processed: 163 average time/residue: 0.1819 time to fit residues: 43.7863 Evaluate side-chains 152 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN B 94 GLN B 562 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9842 Z= 0.228 Angle : 0.733 12.254 13360 Z= 0.373 Chirality : 0.046 0.183 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.646 38.678 1288 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.35 % Favored : 89.47 % Rotamer: Outliers : 4.83 % Allowed : 21.53 % Favored : 73.65 % 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: -4.26 (0.21), residues: 1130 helix: -2.27 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -3.60 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 397 HIS 0.005 0.001 HIS A 824 PHE 0.022 0.002 PHE A 681 TYR 0.027 0.002 TYR B 528 ARG 0.003 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 136 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4665 (OUTLIER) cc_final: 0.3514 (mmtm) REVERT: A 773 MET cc_start: 0.6053 (mmm) cc_final: 0.5782 (mmm) REVERT: B 590 LYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4036 (mmtm) REVERT: B 725 TRP cc_start: 0.6203 (m100) cc_final: 0.5992 (m100) REVERT: B 742 MET cc_start: 0.5324 (mtt) cc_final: 0.4937 (mtp) REVERT: B 764 PRO cc_start: 0.6758 (Cg_endo) cc_final: 0.6458 (Cg_exo) outliers start: 50 outliers final: 36 residues processed: 177 average time/residue: 0.1883 time to fit residues: 49.7816 Evaluate side-chains 160 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 112 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9842 Z= 0.177 Angle : 0.726 12.158 13360 Z= 0.359 Chirality : 0.045 0.226 1480 Planarity : 0.005 0.061 1630 Dihedral : 6.341 37.351 1288 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.73 % Favored : 90.09 % Rotamer: Outliers : 3.47 % Allowed : 23.55 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.22), residues: 1130 helix: -1.94 (0.18), residues: 654 sheet: None (None), residues: 0 loop : -3.61 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 397 HIS 0.002 0.001 HIS A 844 PHE 0.025 0.001 PHE A 125 TYR 0.025 0.001 TYR B 528 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 ASN cc_start: 0.6968 (m-40) cc_final: 0.6221 (m-40) REVERT: A 590 LYS cc_start: 0.4591 (OUTLIER) cc_final: 0.3625 (mmtm) REVERT: B 590 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4313 (mmtm) REVERT: B 725 TRP cc_start: 0.6352 (m100) cc_final: 0.6053 (m100) REVERT: B 764 PRO cc_start: 0.6706 (Cg_endo) cc_final: 0.6412 (Cg_exo) outliers start: 36 outliers final: 26 residues processed: 170 average time/residue: 0.1859 time to fit residues: 46.0844 Evaluate side-chains 153 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9842 Z= 0.259 Angle : 0.782 11.493 13360 Z= 0.393 Chirality : 0.047 0.223 1480 Planarity : 0.005 0.059 1630 Dihedral : 6.491 37.427 1287 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.50 % Favored : 88.32 % Rotamer: Outliers : 3.96 % Allowed : 24.71 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.22), residues: 1130 helix: -1.90 (0.18), residues: 672 sheet: None (None), residues: 0 loop : -3.58 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 397 HIS 0.006 0.001 HIS A 824 PHE 0.026 0.002 PHE B 374 TYR 0.028 0.002 TYR A 306 ARG 0.003 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4896 (OUTLIER) cc_final: 0.3910 (mmtm) REVERT: B 386 MET cc_start: 0.4850 (mmt) cc_final: 0.4602 (mmt) REVERT: B 590 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.4362 (mmtt) REVERT: B 764 PRO cc_start: 0.6787 (Cg_endo) cc_final: 0.6512 (Cg_exo) outliers start: 41 outliers final: 35 residues processed: 166 average time/residue: 0.1894 time to fit residues: 45.8156 Evaluate side-chains 162 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9842 Z= 0.227 Angle : 0.763 11.542 13360 Z= 0.380 Chirality : 0.046 0.230 1480 Planarity : 0.005 0.058 1630 Dihedral : 6.360 36.441 1286 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.29 % Rotamer: Outliers : 3.76 % Allowed : 25.58 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.23), residues: 1130 helix: -1.73 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -3.59 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.004 0.001 HIS A 824 PHE 0.028 0.002 PHE B 374 TYR 0.030 0.002 TYR A 847 ARG 0.006 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4138 (mmtm) REVERT: A 668 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6140 (t80) REVERT: B 386 MET cc_start: 0.4626 (mmt) cc_final: 0.4387 (mmt) REVERT: B 590 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4474 (mmtt) REVERT: B 742 MET cc_start: 0.5033 (mtt) cc_final: 0.4795 (mtp) REVERT: B 750 MET cc_start: 0.6396 (tpt) cc_final: 0.6194 (tpt) REVERT: B 764 PRO cc_start: 0.7081 (Cg_endo) cc_final: 0.6871 (Cg_exo) REVERT: B 773 MET cc_start: 0.6065 (mmm) cc_final: 0.5757 (mmm) outliers start: 39 outliers final: 32 residues processed: 159 average time/residue: 0.1849 time to fit residues: 43.5976 Evaluate side-chains 158 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.0030 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 GLN B 620 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9842 Z= 0.199 Angle : 0.742 11.472 13360 Z= 0.369 Chirality : 0.046 0.211 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.164 35.425 1286 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.06 % Favored : 88.76 % Rotamer: Outliers : 3.76 % Allowed : 25.58 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.23), residues: 1130 helix: -1.53 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.003 0.001 HIS A 824 PHE 0.026 0.002 PHE B 374 TYR 0.043 0.002 TYR B 828 ARG 0.005 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.6865 (pmm) cc_final: 0.6615 (pmm) REVERT: A 590 LYS cc_start: 0.4965 (OUTLIER) cc_final: 0.4158 (mmtm) REVERT: A 668 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.6150 (t80) REVERT: B 386 MET cc_start: 0.4571 (mmt) cc_final: 0.4270 (mmt) REVERT: B 590 LYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4617 (mmtm) REVERT: B 742 MET cc_start: 0.5005 (mtt) cc_final: 0.4795 (mtp) REVERT: B 750 MET cc_start: 0.6452 (tpt) cc_final: 0.6219 (tpt) REVERT: B 764 PRO cc_start: 0.7019 (Cg_endo) cc_final: 0.6815 (Cg_exo) REVERT: B 773 MET cc_start: 0.5953 (mmm) cc_final: 0.5636 (mmm) outliers start: 39 outliers final: 33 residues processed: 164 average time/residue: 0.1711 time to fit residues: 42.1154 Evaluate side-chains 155 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 0.0030 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN B 620 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9842 Z= 0.192 Angle : 0.763 13.909 13360 Z= 0.369 Chirality : 0.045 0.200 1480 Planarity : 0.005 0.062 1630 Dihedral : 5.971 34.716 1286 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 3.19 % Allowed : 26.16 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.23), residues: 1130 helix: -1.40 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.44 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.003 0.001 HIS A 844 PHE 0.026 0.001 PHE B 374 TYR 0.038 0.001 TYR B 828 ARG 0.005 0.000 ARG B 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.5119 (OUTLIER) cc_final: 0.4477 (mmtm) REVERT: A 668 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.6336 (t80) REVERT: B 386 MET cc_start: 0.4701 (mmt) cc_final: 0.4364 (mmt) REVERT: B 590 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4876 (mmtt) REVERT: B 750 MET cc_start: 0.6433 (tpt) cc_final: 0.6196 (tpt) REVERT: B 773 MET cc_start: 0.5725 (mmm) cc_final: 0.5451 (mmm) REVERT: B 842 MET cc_start: 0.7594 (mmt) cc_final: 0.7224 (mmt) outliers start: 33 outliers final: 28 residues processed: 151 average time/residue: 0.1780 time to fit residues: 40.7100 Evaluate side-chains 153 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN B 620 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5572 r_free = 0.5572 target = 0.277125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.246734 restraints weight = 12466.818| |-----------------------------------------------------------------------------| r_work (start): 0.5272 rms_B_bonded: 2.64 r_work: 0.5081 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.5081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9842 Z= 0.195 Angle : 0.750 13.999 13360 Z= 0.366 Chirality : 0.045 0.185 1480 Planarity : 0.005 0.063 1630 Dihedral : 5.894 34.203 1286 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 3.38 % Allowed : 25.87 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.23), residues: 1130 helix: -1.33 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 397 HIS 0.003 0.001 HIS A 824 PHE 0.024 0.001 PHE B 374 TYR 0.033 0.002 TYR B 828 ARG 0.004 0.000 ARG B 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.11 seconds wall clock time: 38 minutes 49.74 seconds (2329.74 seconds total)