Starting phenix.real_space_refine on Thu Feb 15 05:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/02_2024/7dtv_30855.pdb" } resolution = 3.5 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= 0.003 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 4 9.91 5 S 46 5.16 5 C 7126 2.51 5 N 1940 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 30, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 Chain: "B" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 30, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.26, per 1000 atoms: 0.56 Number of scatterers: 11276 At special positions: 0 Unit cell: (90.246, 94.302, 179.478, 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 4 19.99 S 46 16.00 O 2160 8.00 N 1940 7.00 C 7126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.14 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.20 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.02 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.02 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.14 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.20 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.02 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.02 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A1104 " - " ASN A 261 " " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 446 " " NAG A1107 " - " ASN A 468 " " NAG B1103 " - " ASN B 261 " " NAG B1104 " - " ASN B 287 " " NAG B1105 " - " ASN B 446 " " NAG B1106 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 41.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.728A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.516A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.721A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 433 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.597A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE A 533 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.320A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 858 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.727A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.517A pdb=" N GLU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.722A pdb=" N LYS B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 433 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.598A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE B 533 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.321A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 830 through 835' Processing helix chain 'B' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 858 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 495 Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA A 600 " --> pdb=" O TRP A 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AB7, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AB9, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA B 600 " --> pdb=" O TRP B 590 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1134 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: 3.74 Time building geometry restraints manager: 4.44 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: 3683 1.34 - 1.46: 2278 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 11504 Sorted by residual: bond pdb=" C1 NAG B1105 " pdb=" O5 NAG B1105 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1106 " pdb=" O5 NAG A1106 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1104 " pdb=" O5 NAG A1104 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG D 3 " pdb=" O5 NAG D 3 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 ... (remaining 11499 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.53: 306 106.53 - 113.44: 6242 113.44 - 120.34: 4424 120.34 - 127.25: 4613 127.25 - 134.16: 119 Bond angle restraints: 15704 Sorted by residual: angle pdb=" N ASP B 570 " pdb=" CA ASP B 570 " pdb=" C ASP B 570 " ideal model delta sigma weight residual 111.02 120.03 -9.01 1.25e+00 6.40e-01 5.19e+01 angle pdb=" N ASP A 570 " pdb=" CA ASP A 570 " pdb=" C ASP A 570 " ideal model delta sigma weight residual 111.02 120.01 -8.99 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N PHE B 128 " pdb=" CA PHE B 128 " pdb=" C PHE B 128 " ideal model delta sigma weight residual 111.37 120.19 -8.82 1.64e+00 3.72e-01 2.89e+01 angle pdb=" N PHE A 128 " pdb=" CA PHE A 128 " pdb=" C PHE A 128 " ideal model delta sigma weight residual 111.37 120.17 -8.80 1.64e+00 3.72e-01 2.88e+01 angle pdb=" N GLU B 127 " pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 110.80 100.68 10.12 2.13e+00 2.20e-01 2.26e+01 ... (remaining 15699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 6219 17.46 - 34.92: 643 34.92 - 52.38: 130 52.38 - 69.84: 32 69.84 - 87.30: 8 Dihedral angle restraints: 7032 sinusoidal: 2508 harmonic: 4524 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 157.37 -64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 7029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1838 0.256 - 0.511: 6 0.511 - 0.767: 0 0.767 - 1.023: 0 1.023 - 1.278: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 488 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.09e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 488 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.08e+01 chirality pdb=" CA CYS A 765 " pdb=" N CYS A 765 " pdb=" C CYS A 765 " pdb=" CB CYS A 765 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1843 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 797 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO B 798 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 797 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 798 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 798 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 798 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 610 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.63e+00 pdb=" N PRO A 611 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.035 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 879 2.73 - 3.27: 10480 3.27 - 3.82: 17494 3.82 - 4.36: 20337 4.36 - 4.90: 35982 Nonbonded interactions: 85172 Sorted by model distance: nonbonded pdb=" OE2 GLU B 282 " pdb=" CD ARG B 286 " model vdw 2.189 3.440 nonbonded pdb=" OE2 GLU A 282 " pdb=" CD ARG A 286 " model vdw 2.189 3.440 nonbonded pdb=" O ALA A 144 " pdb=" OG SER A 150 " model vdw 2.207 2.440 nonbonded pdb=" O ALA B 144 " pdb=" OG SER B 150 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR B 218 " pdb=" OG SER B 296 " model vdw 2.215 2.440 ... (remaining 85167 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' and (resid 20 through 859 or resid 1101 through 1102 or resid 1104 th \ rough 1106)) selection = (chain 'B' and (resid 20 through 859 or resid 1101 through 1102 or resid 1104 th \ rough 1106)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.030 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.540 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.008 0.079 11504 Z= 0.533 Angle : 0.937 10.120 15704 Z= 0.528 Chirality : 0.074 1.278 1846 Planarity : 0.007 0.079 2046 Dihedral : 14.961 87.299 4046 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 17.58 % Favored : 82.42 % 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: -4.67 (0.17), residues: 1542 helix: -2.99 (0.15), residues: 604 sheet: -3.32 (0.35), residues: 158 loop : -3.15 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 299 HIS 0.003 0.001 HIS A 312 PHE 0.014 0.002 PHE A 539 TYR 0.013 0.002 TYR A 63 ARG 0.002 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.253 Fit side-chains REVERT: A 74 MET cc_start: 0.8954 (ttt) cc_final: 0.8717 (ttt) REVERT: B 74 MET cc_start: 0.8961 (ttt) cc_final: 0.8720 (ttt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2429 time to fit residues: 39.8633 Evaluate side-chains 79 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 193 GLN A 466 HIS A 476 GLN B 72 GLN B 90 ASN B 193 GLN B 466 HIS B 476 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11504 Z= 0.228 Angle : 0.611 8.068 15704 Z= 0.317 Chirality : 0.054 0.756 1846 Planarity : 0.004 0.044 2046 Dihedral : 10.166 116.855 2020 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.91 % Allowed : 21.08 % Favored : 77.01 % 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: -3.44 (0.19), residues: 1542 helix: -1.53 (0.19), residues: 604 sheet: -3.00 (0.35), residues: 158 loop : -2.76 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.003 0.001 HIS B 463 PHE 0.011 0.001 PHE A 589 TYR 0.014 0.001 TYR A 510 ARG 0.002 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.221 Fit side-chains REVERT: A 74 MET cc_start: 0.8905 (ttt) cc_final: 0.8595 (ttt) REVERT: A 282 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 307 MET cc_start: 0.8426 (mtp) cc_final: 0.8073 (mtt) REVERT: A 359 HIS cc_start: 0.7621 (t70) cc_final: 0.7242 (t70) REVERT: B 74 MET cc_start: 0.8897 (ttt) cc_final: 0.8583 (ttt) REVERT: B 282 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 307 MET cc_start: 0.8416 (mtp) cc_final: 0.8064 (mtt) REVERT: B 359 HIS cc_start: 0.7614 (t70) cc_final: 0.7236 (t70) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.1985 time to fit residues: 31.1728 Evaluate side-chains 92 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 524 ASN B 253 GLN B 524 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11504 Z= 0.273 Angle : 0.569 6.324 15704 Z= 0.301 Chirality : 0.046 0.219 1846 Planarity : 0.004 0.041 2046 Dihedral : 9.623 118.913 2020 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.81 % Allowed : 20.97 % Favored : 75.21 % 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: -2.84 (0.20), residues: 1542 helix: -0.92 (0.20), residues: 608 sheet: -2.68 (0.38), residues: 158 loop : -2.53 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.002 0.001 HIS A 463 PHE 0.008 0.001 PHE B 589 TYR 0.020 0.001 TYR A 510 ARG 0.005 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8495 (mtp) cc_final: 0.8072 (mtt) REVERT: A 359 HIS cc_start: 0.7658 (t70) cc_final: 0.7245 (t70) REVERT: B 307 MET cc_start: 0.8489 (mtp) cc_final: 0.8082 (mtt) REVERT: B 359 HIS cc_start: 0.7644 (t70) cc_final: 0.7226 (t70) outliers start: 36 outliers final: 30 residues processed: 116 average time/residue: 0.1856 time to fit residues: 33.9357 Evaluate side-chains 107 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11504 Z= 0.439 Angle : 0.631 5.978 15704 Z= 0.331 Chirality : 0.048 0.233 1846 Planarity : 0.004 0.048 2046 Dihedral : 9.692 117.698 2020 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.77 % Allowed : 20.55 % Favored : 74.68 % 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: -2.59 (0.21), residues: 1542 helix: -0.67 (0.21), residues: 608 sheet: -2.65 (0.38), residues: 158 loop : -2.41 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 675 HIS 0.004 0.001 HIS A 413 PHE 0.011 0.001 PHE B 42 TYR 0.017 0.002 TYR A 510 ARG 0.006 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 79 time to evaluate : 1.267 Fit side-chains REVERT: A 220 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7871 (ttm110) REVERT: A 359 HIS cc_start: 0.7735 (t70) cc_final: 0.7284 (t70) REVERT: B 220 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7866 (ttm110) REVERT: B 359 HIS cc_start: 0.7729 (t70) cc_final: 0.7261 (t70) outliers start: 45 outliers final: 33 residues processed: 116 average time/residue: 0.1980 time to fit residues: 35.2217 Evaluate side-chains 113 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 595 HIS B 338 HIS B 595 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11504 Z= 0.165 Angle : 0.518 6.079 15704 Z= 0.273 Chirality : 0.044 0.206 1846 Planarity : 0.003 0.032 2046 Dihedral : 9.065 116.679 2020 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.50 % Allowed : 23.73 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1542 helix: -0.03 (0.21), residues: 592 sheet: -2.26 (0.43), residues: 130 loop : -2.26 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.001 0.000 HIS A 312 PHE 0.006 0.001 PHE B 160 TYR 0.017 0.001 TYR A 510 ARG 0.004 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8425 (mtp) cc_final: 0.8042 (mtt) REVERT: A 359 HIS cc_start: 0.7691 (t70) cc_final: 0.7279 (t70) REVERT: B 307 MET cc_start: 0.8431 (mtp) cc_final: 0.8057 (mtt) REVERT: B 359 HIS cc_start: 0.7702 (t70) cc_final: 0.7288 (t70) outliers start: 33 outliers final: 25 residues processed: 123 average time/residue: 0.1757 time to fit residues: 34.6362 Evaluate side-chains 116 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11504 Z= 0.218 Angle : 0.523 6.271 15704 Z= 0.274 Chirality : 0.045 0.217 1846 Planarity : 0.003 0.031 2046 Dihedral : 8.863 115.915 2020 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.92 % Allowed : 22.46 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1542 helix: 0.24 (0.22), residues: 594 sheet: -2.14 (0.44), residues: 130 loop : -2.16 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 463 PHE 0.008 0.001 PHE B 68 TYR 0.015 0.001 TYR A 435 ARG 0.002 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8510 (mtp) cc_final: 0.8077 (mtt) REVERT: A 359 HIS cc_start: 0.7691 (t70) cc_final: 0.7260 (t70) REVERT: A 846 PHE cc_start: 0.8506 (t80) cc_final: 0.8242 (t80) REVERT: B 307 MET cc_start: 0.8477 (mtp) cc_final: 0.8043 (mtt) REVERT: B 359 HIS cc_start: 0.7673 (t70) cc_final: 0.7232 (t70) outliers start: 37 outliers final: 31 residues processed: 121 average time/residue: 0.1813 time to fit residues: 35.1642 Evaluate side-chains 123 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11504 Z= 0.226 Angle : 0.518 6.176 15704 Z= 0.271 Chirality : 0.044 0.205 1846 Planarity : 0.003 0.030 2046 Dihedral : 8.713 116.049 2020 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.28 % Allowed : 23.31 % Favored : 73.41 % 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: -1.59 (0.21), residues: 1542 helix: 0.47 (0.22), residues: 582 sheet: -2.08 (0.44), residues: 140 loop : -2.08 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS B 463 PHE 0.009 0.001 PHE B 270 TYR 0.014 0.001 TYR A 510 ARG 0.002 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8529 (mtp) cc_final: 0.8068 (mtt) REVERT: A 359 HIS cc_start: 0.7697 (t70) cc_final: 0.7261 (t70) REVERT: A 846 PHE cc_start: 0.8478 (t80) cc_final: 0.8189 (t80) REVERT: B 307 MET cc_start: 0.8515 (mtp) cc_final: 0.8052 (mtt) REVERT: B 359 HIS cc_start: 0.7690 (t70) cc_final: 0.7251 (t70) outliers start: 31 outliers final: 31 residues processed: 121 average time/residue: 0.1800 time to fit residues: 34.9528 Evaluate side-chains 121 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11504 Z= 0.204 Angle : 0.502 6.332 15704 Z= 0.262 Chirality : 0.044 0.203 1846 Planarity : 0.003 0.030 2046 Dihedral : 8.416 114.995 2020 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.81 % Allowed : 23.20 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1542 helix: 0.69 (0.22), residues: 576 sheet: -2.01 (0.44), residues: 140 loop : -2.01 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 352 HIS 0.002 0.000 HIS B 312 PHE 0.009 0.001 PHE A 821 TYR 0.013 0.001 TYR A 510 ARG 0.003 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7850 (ttm110) REVERT: A 307 MET cc_start: 0.8523 (mtp) cc_final: 0.8053 (mtt) REVERT: A 359 HIS cc_start: 0.7668 (t70) cc_final: 0.7219 (t70) REVERT: A 846 PHE cc_start: 0.8419 (t80) cc_final: 0.8200 (t80) REVERT: B 307 MET cc_start: 0.8517 (mtp) cc_final: 0.8039 (mtt) REVERT: B 359 HIS cc_start: 0.7663 (t70) cc_final: 0.7217 (t70) REVERT: B 846 PHE cc_start: 0.8419 (t80) cc_final: 0.8183 (t80) outliers start: 36 outliers final: 35 residues processed: 121 average time/residue: 0.1924 time to fit residues: 36.4703 Evaluate side-chains 124 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.1980 chunk 129 optimal weight: 0.3980 chunk 138 optimal weight: 0.0870 chunk 83 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11504 Z= 0.136 Angle : 0.474 6.528 15704 Z= 0.248 Chirality : 0.043 0.195 1846 Planarity : 0.003 0.031 2046 Dihedral : 8.141 113.913 2020 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.65 % Allowed : 24.68 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1542 helix: 0.88 (0.22), residues: 576 sheet: -1.85 (0.44), residues: 140 loop : -1.95 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.002 0.000 HIS A 312 PHE 0.011 0.001 PHE A 821 TYR 0.014 0.001 TYR A 510 ARG 0.003 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8586 (mtp) cc_final: 0.8107 (mtt) REVERT: A 359 HIS cc_start: 0.7656 (t70) cc_final: 0.7213 (t70) REVERT: B 307 MET cc_start: 0.8580 (mtp) cc_final: 0.8100 (mtt) REVERT: B 359 HIS cc_start: 0.7657 (t70) cc_final: 0.7205 (t70) REVERT: B 846 PHE cc_start: 0.8422 (t80) cc_final: 0.8205 (t80) outliers start: 25 outliers final: 24 residues processed: 121 average time/residue: 0.1860 time to fit residues: 35.9047 Evaluate side-chains 119 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11504 Z= 0.265 Angle : 0.523 6.574 15704 Z= 0.272 Chirality : 0.045 0.206 1846 Planarity : 0.003 0.029 2046 Dihedral : 8.222 113.775 2020 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.28 % Allowed : 24.58 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1542 helix: 0.89 (0.22), residues: 576 sheet: -1.93 (0.45), residues: 140 loop : -1.94 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 675 HIS 0.002 0.001 HIS B 463 PHE 0.012 0.001 PHE A 846 TYR 0.011 0.001 TYR A 510 ARG 0.003 0.000 ARG B 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8550 (mtp) cc_final: 0.8050 (mtt) REVERT: A 359 HIS cc_start: 0.7677 (t70) cc_final: 0.7214 (t70) REVERT: B 307 MET cc_start: 0.8551 (mtp) cc_final: 0.8054 (mtt) REVERT: B 359 HIS cc_start: 0.7670 (t70) cc_final: 0.7201 (t70) REVERT: B 846 PHE cc_start: 0.8422 (t80) cc_final: 0.8193 (t80) outliers start: 31 outliers final: 31 residues processed: 112 average time/residue: 0.1765 time to fit residues: 31.6267 Evaluate side-chains 118 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137383 restraints weight = 14639.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124570 restraints weight = 20411.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123188 restraints weight = 25229.551| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11504 Z= 0.241 Angle : 0.516 6.563 15704 Z= 0.270 Chirality : 0.044 0.207 1846 Planarity : 0.003 0.030 2046 Dihedral : 8.214 113.727 2020 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.50 % Allowed : 24.26 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1542 helix: 0.89 (0.22), residues: 578 sheet: -1.91 (0.45), residues: 140 loop : -1.94 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 675 HIS 0.002 0.001 HIS A 463 PHE 0.011 0.001 PHE A 821 TYR 0.012 0.001 TYR A 510 ARG 0.003 0.000 ARG B 551 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.80 seconds wall clock time: 38 minutes 26.39 seconds (2306.39 seconds total)