Starting phenix.real_space_refine (version: dev) on Mon Dec 12 07:47:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2022/6p49_20247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2022/6p49_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_20247/12_2022/6p49_20247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2022/6p49_20247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2022/6p49_20247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2022/6p49_20247.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.67, per 1000 atoms: 0.59 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: 3.94 Conformation dependent library (CDL) restraints added in 1.6 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: 0.34 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: 2.24 Time building geometry restraints manager: 4.07 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 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. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.000 Extract box with map and model: 4.630 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.070 Process input model: 26.320 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 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 % 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 *********************** 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 : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 10 residues processed: 222 average time/residue: 0.2370 time to fit residues: 71.0812 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1127 time to fit residues: 3.4339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0010 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 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: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.5721 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9842 Z= 0.216 Angle : 0.813 11.749 13360 Z= 0.418 Chirality : 0.047 0.220 1480 Planarity : 0.007 0.066 1630 Dihedral : 7.272 27.695 1278 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.03 % Favored : 90.80 % Rotamer Outliers : 2.41 % 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: -5.19 (0.19), residues: 1130 helix: -3.13 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -3.82 (0.21), residues: 498 *********************** 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 182 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 174 average time/residue: 0.1989 time to fit residues: 49.4164 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0888 time to fit residues: 3.3479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 0.0030 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 608 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.3401 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= 0.191 Angle : 0.730 14.964 13360 Z= 0.373 Chirality : 0.045 0.202 1480 Planarity : 0.006 0.062 1630 Dihedral : 6.631 26.916 1278 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.09 % Favored : 89.65 % Rotamer Outliers : 2.03 % 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: -4.73 (0.20), residues: 1130 helix: -2.69 (0.17), residues: 650 sheet: None (None), residues: 0 loop : -3.74 (0.22), residues: 480 *********************** 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 161 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 154 average time/residue: 0.1897 time to fit residues: 43.1635 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1066 time to fit residues: 3.8977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** 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: 0.5768 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9842 Z= 0.213 Angle : 0.722 13.223 13360 Z= 0.367 Chirality : 0.045 0.176 1480 Planarity : 0.005 0.062 1630 Dihedral : 6.384 26.542 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.73 % Favored : 90.09 % Rotamer Outliers : 1.93 % 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: -4.47 (0.21), residues: 1130 helix: -2.42 (0.17), residues: 656 sheet: None (None), residues: 0 loop : -3.73 (0.23), residues: 474 *********************** 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 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 145 average time/residue: 0.1808 time to fit residues: 39.1220 Evaluate side-chains 132 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0905 time to fit residues: 3.5122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 620 ASN B 94 GLN B 562 ASN B 726 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9842 Z= 0.237 Angle : 0.729 12.290 13360 Z= 0.376 Chirality : 0.045 0.181 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.329 26.162 1278 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.80 % Favored : 89.03 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.21), residues: 1130 helix: -2.24 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -3.69 (0.24), residues: 474 *********************** 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 161 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 157 average time/residue: 0.1821 time to fit residues: 43.1875 Evaluate side-chains 139 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1030 time to fit residues: 4.5087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 608 GLN A 844 HIS B 94 GLN B 844 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9842 Z= 0.203 Angle : 0.721 12.174 13360 Z= 0.364 Chirality : 0.045 0.203 1480 Planarity : 0.005 0.059 1630 Dihedral : 6.170 25.276 1278 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.27 % Favored : 89.56 % Rotamer Outliers : 1.93 % 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: -4.01 (0.22), residues: 1130 helix: -1.98 (0.18), residues: 672 sheet: None (None), residues: 0 loop : -3.68 (0.25), residues: 458 *********************** 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 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.1919 time to fit residues: 43.7360 Evaluate side-chains 131 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0946 time to fit residues: 3.4643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 608 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.4705 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= 0.193 Angle : 0.729 11.751 13360 Z= 0.363 Chirality : 0.045 0.263 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.008 24.258 1278 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.44 % Favored : 89.38 % Rotamer Outliers : 0.68 % 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: -3.70 (0.23), residues: 1130 helix: -1.68 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -3.64 (0.25), residues: 460 *********************** 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 139 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 138 average time/residue: 0.1833 time to fit residues: 37.6290 Evaluate side-chains 129 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0830 time to fit residues: 1.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9842 Z= 0.201 Angle : 0.729 12.741 13360 Z= 0.363 Chirality : 0.045 0.204 1480 Planarity : 0.005 0.059 1630 Dihedral : 5.918 23.408 1278 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.35 % Favored : 89.47 % Rotamer Outliers : 0.97 % 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: -3.53 (0.23), residues: 1130 helix: -1.56 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -3.54 (0.25), residues: 458 *********************** 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 140 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.1854 time to fit residues: 38.2177 Evaluate side-chains 129 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0971 time to fit residues: 2.6259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 620 ASN B 621 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 9842 Z= 0.291 Angle : 0.801 13.728 13360 Z= 0.404 Chirality : 0.047 0.192 1480 Planarity : 0.005 0.057 1630 Dihedral : 6.194 24.574 1278 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.50 % Favored : 88.41 % Rotamer Outliers : 0.39 % 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: -3.62 (0.23), residues: 1130 helix: -1.62 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -3.57 (0.25), residues: 464 *********************** 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 128 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 127 average time/residue: 0.1706 time to fit residues: 32.9347 Evaluate side-chains 119 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0855 time to fit residues: 1.8411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 73 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 562 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN B 620 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.5389 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= 0.183 Angle : 0.739 15.620 13360 Z= 0.364 Chirality : 0.045 0.207 1480 Planarity : 0.005 0.061 1630 Dihedral : 5.848 23.377 1278 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer Outliers : 0.29 % 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: -3.35 (0.23), residues: 1130 helix: -1.41 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 460 ********************** 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 134 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.1830 time to fit residues: 36.3065 Evaluate side-chains 122 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0856 time to fit residues: 1.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 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 = 0.5595 r_free = 0.5595 target = 0.279407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.249789 restraints weight = 12685.237| |-----------------------------------------------------------------------------| r_work (start): 0.5292 rms_B_bonded: 2.59 r_work: 0.5098 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.5523 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= 0.185 Angle : 0.728 15.174 13360 Z= 0.358 Chirality : 0.044 0.196 1480 Planarity : 0.005 0.062 1630 Dihedral : 5.684 24.314 1278 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 0.29 % 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: -1.31 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -3.46 (0.26), residues: 458 =============================================================================== Job complete usr+sys time: 1984.72 seconds wall clock time: 36 minutes 54.31 seconds (2214.31 seconds total)