Starting phenix.real_space_refine on Sat Dec 9 00:42:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2023/6p49_20247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2023/6p49_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_2023/6p49_20247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2023/6p49_20247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2023/6p49_20247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/12_2023/6p49_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.28, 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: 3.65 Conformation dependent library (CDL) restraints added in 1.8 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: 0.89 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: 2.42 Time building geometry restraints manager: 3.92 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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 : 1.074 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: 0.2492 time to fit residues: 74.2114 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1161 time to fit residues: 3.4130 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 0.9990 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: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.5743 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9842 Z= 0.239 Angle : 0.825 11.571 13360 Z= 0.426 Chirality : 0.047 0.191 1480 Planarity : 0.007 0.066 1630 Dihedral : 7.374 28.227 1278 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 2.51 % Allowed : 17.18 % Favored : 80.31 % 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 (0.22), 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 0.018 0.002 PHE A 556 TYR 0.020 0.002 TYR B 847 ARG 0.009 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 181 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 173 average time/residue: 0.2159 time to fit residues: 53.3799 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0914 time to fit residues: 3.4783 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9842 Z= 0.227 Angle : 0.760 15.144 13360 Z= 0.391 Chirality : 0.046 0.197 1480 Planarity : 0.006 0.064 1630 Dihedral : 6.848 27.673 1278 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.27 % Favored : 89.56 % Rotamer: Outliers : 2.12 % Allowed : 20.75 % Favored : 77.12 % 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: -4.79 (0.20), residues: 1130 helix: -2.80 (0.16), residues: 660 sheet: None (None), residues: 0 loop : -3.67 (0.23), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.005 0.001 HIS A 824 PHE 0.023 0.002 PHE B 556 TYR 0.023 0.002 TYR A 306 ARG 0.005 0.000 ARG B 592 *********************** 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 165 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.2155 time to fit residues: 52.0760 Evaluate side-chains 134 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 2.458 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1137 time to fit residues: 4.7662 ------------------------------------------------------------------------------- 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: 3.9990 chunk 79 optimal weight: 0.0070 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9842 Z= 0.258 Angle : 0.766 12.830 13360 Z= 0.394 Chirality : 0.046 0.181 1480 Planarity : 0.006 0.058 1630 Dihedral : 6.684 28.408 1278 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.27 % Favored : 89.56 % Rotamer: Outliers : 2.90 % Allowed : 22.39 % Favored : 74.71 % 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: -4.56 (0.20), residues: 1130 helix: -2.53 (0.17), residues: 654 sheet: None (None), residues: 0 loop : -3.70 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 302 HIS 0.005 0.001 HIS A 824 PHE 0.027 0.002 PHE B 681 TYR 0.026 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 162 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 155 average time/residue: 0.1729 time to fit residues: 40.8938 Evaluate side-chains 144 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0955 time to fit residues: 4.9613 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 28 optimal weight: 0.0270 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN A 844 HIS B 94 GLN B 726 GLN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9842 Z= 0.181 Angle : 0.708 12.938 13360 Z= 0.358 Chirality : 0.044 0.178 1480 Planarity : 0.005 0.056 1630 Dihedral : 6.216 25.799 1278 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.82 % Favored : 90.00 % Rotamer: Outliers : 1.64 % Allowed : 23.07 % Favored : 75.29 % 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: -4.18 (0.21), residues: 1130 helix: -2.15 (0.18), residues: 656 sheet: None (None), residues: 0 loop : -3.66 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 397 HIS 0.002 0.001 HIS B 824 PHE 0.023 0.001 PHE B 681 TYR 0.018 0.001 TYR A 306 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 163 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 160 average time/residue: 0.1825 time to fit residues: 43.9008 Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.052 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.0982 time to fit residues: 3.3001 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN A 844 HIS B 844 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.4591 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= 0.178 Angle : 0.715 12.182 13360 Z= 0.355 Chirality : 0.044 0.172 1480 Planarity : 0.005 0.057 1630 Dihedral : 5.974 23.828 1278 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 1.64 % Allowed : 25.19 % Favored : 73.17 % 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: -3.87 (0.22), residues: 1130 helix: -1.82 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.68 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 397 HIS 0.004 0.001 HIS A 844 PHE 0.026 0.001 PHE A 125 TYR 0.024 0.001 TYR B 847 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 154 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.1830 time to fit residues: 40.4451 Evaluate side-chains 135 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0855 time to fit residues: 2.9820 ------------------------------------------------------------------------------- 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: 0.3980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 111 optimal weight: 0.0170 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 GLN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.4872 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= 0.172 Angle : 0.715 11.686 13360 Z= 0.352 Chirality : 0.044 0.189 1480 Planarity : 0.005 0.060 1630 Dihedral : 5.815 23.146 1278 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.38 % Favored : 90.44 % Rotamer: Outliers : 0.48 % Allowed : 26.25 % Favored : 73.26 % 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: -3.57 (0.23), residues: 1130 helix: -1.59 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -3.57 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 397 HIS 0.003 0.001 HIS B 844 PHE 0.020 0.001 PHE A 681 TYR 0.022 0.001 TYR B 847 ARG 0.003 0.000 ARG B 753 *********************** 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 145 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.1860 time to fit residues: 39.2913 Evaluate side-chains 129 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1107 time to fit residues: 1.9212 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.5711 moved from start: 0.5047 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= 0.194 Angle : 0.724 11.420 13360 Z= 0.359 Chirality : 0.045 0.200 1480 Planarity : 0.005 0.063 1630 Dihedral : 5.756 22.173 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.35 % Favored : 89.47 % Rotamer: Outliers : 0.58 % Allowed : 27.22 % Favored : 72.20 % 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: -3.40 (0.23), residues: 1130 helix: -1.41 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 466 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 0.019 0.001 PHE A 681 TYR 0.030 0.001 TYR A 847 ARG 0.003 0.000 ARG B 542 *********************** 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 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 0.1919 time to fit residues: 38.1008 Evaluate side-chains 123 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0963 time to fit residues: 2.1563 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.5818 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9842 Z= 0.244 Angle : 0.753 11.089 13360 Z= 0.380 Chirality : 0.046 0.180 1480 Planarity : 0.005 0.060 1630 Dihedral : 5.961 22.708 1278 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.50 % Favored : 88.32 % Rotamer: Outliers : 0.87 % Allowed : 26.25 % Favored : 72.88 % 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: -1.53 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -3.59 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 397 HIS 0.005 0.001 HIS A 824 PHE 0.021 0.002 PHE A 556 TYR 0.041 0.002 TYR B 828 ARG 0.003 0.000 ARG A 753 *********************** 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 138 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 0.1760 time to fit residues: 36.2146 Evaluate side-chains 124 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1002 time to fit residues: 2.5531 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 0.0270 chunk 98 optimal weight: 0.0170 chunk 28 optimal weight: 0.1980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 820 GLN B 351 GLN B 820 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5666 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 0.048 9842 Z= 0.178 Angle : 0.733 14.347 13360 Z= 0.362 Chirality : 0.044 0.180 1480 Planarity : 0.005 0.067 1630 Dihedral : 5.675 22.073 1278 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.39 % Allowed : 27.12 % Favored : 72.49 % 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: -3.24 (0.23), residues: 1130 helix: -1.26 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 397 HIS 0.002 0.001 HIS B 824 PHE 0.027 0.001 PHE B 851 TYR 0.043 0.001 TYR B 828 ARG 0.003 0.000 ARG B 542 ********************** 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 137 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.1855 time to fit residues: 37.5257 Evaluate side-chains 124 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0949 time to fit residues: 1.8901 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.0050 chunk 66 optimal weight: 0.0770 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 362 ASN B 351 GLN B 620 ASN ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5615 r_free = 0.5615 target = 0.281772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.251726 restraints weight = 12563.986| |-----------------------------------------------------------------------------| r_work (start): 0.5305 rms_B_bonded: 2.73 r_work: 0.5108 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.5108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9842 Z= 0.173 Angle : 0.709 11.199 13360 Z= 0.353 Chirality : 0.044 0.185 1480 Planarity : 0.005 0.067 1630 Dihedral : 5.520 22.659 1278 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.29 % Allowed : 27.41 % Favored : 72.30 % 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: -3.14 (0.23), residues: 1130 helix: -1.13 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -3.55 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.002 0.001 HIS A 824 PHE 0.038 0.002 PHE B 851 TYR 0.044 0.001 TYR B 828 ARG 0.003 0.000 ARG B 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.93 seconds wall clock time: 40 minutes 38.91 seconds (2438.91 seconds total)