Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 03:00:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/04_2023/7dtv_30855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/04_2023/7dtv_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_30855/04_2023/7dtv_30855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/04_2023/7dtv_30855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/04_2023/7dtv_30855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/04_2023/7dtv_30855.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-1.21rc1-4938/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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 6.01, per 1000 atoms: 0.53 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: 4.28 Conformation dependent library (CDL) restraints added in 1.9 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: 0.84 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: 3.25 Time building geometry restraints manager: 4.63 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: 5909 17.46 - 34.92: 597 34.92 - 52.38: 114 52.38 - 69.84: 26 69.84 - 87.30: 8 Dihedral angle restraints: 6654 sinusoidal: 2130 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 6651 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: 1.590 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: 7.450 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.010 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- 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 : 14.927 87.299 3668 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 % 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 *********************** 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 : 1.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2404 time to fit residues: 39.5578 Evaluate side-chains 79 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7482 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.5980 chunk 139 optimal weight: 7.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.1062 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= 0.234 Angle : 0.610 6.957 15704 Z= 0.317 Chirality : 0.053 0.694 1846 Planarity : 0.004 0.044 2046 Dihedral : 5.327 24.623 1642 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 1.91 % 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: -3.46 (0.19), residues: 1542 helix: -1.55 (0.19), residues: 604 sheet: -3.00 (0.35), residues: 158 loop : -2.77 (0.20), residues: 780 *********************** 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 : 1.568 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.2053 time to fit residues: 32.4236 Evaluate side-chains 91 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1073 time to fit residues: 4.1684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.1392 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= 0.244 Angle : 0.564 6.148 15704 Z= 0.297 Chirality : 0.046 0.258 1846 Planarity : 0.004 0.042 2046 Dihedral : 4.954 20.324 1642 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 2.54 % 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: -2.82 (0.20), residues: 1542 helix: -0.91 (0.20), residues: 608 sheet: -2.63 (0.38), residues: 158 loop : -2.53 (0.20), residues: 776 *********************** 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 114 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 110 average time/residue: 0.1891 time to fit residues: 33.2584 Evaluate side-chains 98 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1111 time to fit residues: 5.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 66 optimal weight: 0.0040 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 0.0000 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11504 Z= 0.220 Angle : 0.530 5.480 15704 Z= 0.279 Chirality : 0.045 0.264 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.576 18.908 1642 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 2.54 % 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: -2.34 (0.21), residues: 1542 helix: -0.37 (0.21), residues: 606 sheet: -2.50 (0.39), residues: 158 loop : -2.34 (0.21), residues: 778 *********************** 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 111 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 1.187 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 109 average time/residue: 0.1742 time to fit residues: 30.5797 Evaluate side-chains 98 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1042 time to fit residues: 4.6794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1785 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= 0.249 Angle : 0.532 5.442 15704 Z= 0.279 Chirality : 0.045 0.246 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.481 19.289 1642 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 1.17 % 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: -2.02 (0.21), residues: 1542 helix: 0.01 (0.21), residues: 594 sheet: -2.38 (0.39), residues: 158 loop : -2.24 (0.21), residues: 790 *********************** 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 102 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 0.2110 time to fit residues: 31.3661 Evaluate side-chains 88 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1087 time to fit residues: 2.7075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11504 Z= 0.250 Angle : 0.537 6.383 15704 Z= 0.282 Chirality : 0.045 0.252 1846 Planarity : 0.003 0.031 2046 Dihedral : 4.411 20.804 1642 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 1.38 % 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: -1.83 (0.21), residues: 1542 helix: 0.22 (0.22), residues: 594 sheet: -2.31 (0.40), residues: 158 loop : -2.16 (0.21), residues: 790 *********************** 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 99 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.2050 time to fit residues: 30.2403 Evaluate side-chains 88 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1058 time to fit residues: 3.0760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 8.9990 chunk 16 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 83 optimal weight: 0.0770 chunk 148 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11504 Z= 0.148 Angle : 0.482 5.452 15704 Z= 0.254 Chirality : 0.043 0.242 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.100 19.549 1642 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.64 % 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: -1.50 (0.21), residues: 1542 helix: 0.56 (0.22), residues: 594 sheet: -1.96 (0.45), residues: 130 loop : -2.09 (0.21), residues: 818 *********************** 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 98 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 98 average time/residue: 0.1936 time to fit residues: 30.0842 Evaluate side-chains 89 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1260 time to fit residues: 2.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11504 Z= 0.271 Angle : 0.528 5.523 15704 Z= 0.276 Chirality : 0.045 0.251 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.231 18.756 1642 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.85 % 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: -1.44 (0.22), residues: 1542 helix: 0.72 (0.22), residues: 578 sheet: -2.02 (0.44), residues: 140 loop : -2.08 (0.21), residues: 824 *********************** 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 98 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.2006 time to fit residues: 30.2499 Evaluate side-chains 91 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1016 time to fit residues: 3.0407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.0030 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11504 Z= 0.169 Angle : 0.493 5.857 15704 Z= 0.257 Chirality : 0.044 0.242 1846 Planarity : 0.003 0.030 2046 Dihedral : 4.026 19.113 1642 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 0.42 % 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: -1.22 (0.22), residues: 1542 helix: 0.94 (0.22), residues: 576 sheet: -1.89 (0.44), residues: 140 loop : -1.98 (0.21), residues: 826 *********************** 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 98 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.2050 time to fit residues: 30.8907 Evaluate side-chains 91 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1091 time to fit residues: 2.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 69 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 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: 0.7976 moved from start: 0.2253 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= 0.205 Angle : 0.500 5.448 15704 Z= 0.262 Chirality : 0.044 0.245 1846 Planarity : 0.003 0.029 2046 Dihedral : 4.029 18.214 1642 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.42 % 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: -1.17 (0.22), residues: 1542 helix: 0.99 (0.22), residues: 574 sheet: -1.88 (0.44), residues: 140 loop : -1.95 (0.21), residues: 828 ********************** 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 96 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 0.2044 time to fit residues: 30.3767 Evaluate side-chains 94 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1087 time to fit residues: 2.0976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.163961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139195 restraints weight = 14667.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138168 restraints weight = 25186.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138901 restraints weight = 26073.624| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2323 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= 0.186 Angle : 0.492 5.463 15704 Z= 0.257 Chirality : 0.044 0.241 1846 Planarity : 0.003 0.029 2046 Dihedral : 3.941 18.588 1642 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 0.11 % 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: -1.10 (0.22), residues: 1542 helix: 1.07 (0.22), residues: 574 sheet: -1.83 (0.44), residues: 140 loop : -1.92 (0.21), residues: 828 =============================================================================== Job complete usr+sys time: 1821.54 seconds wall clock time: 34 minutes 13.28 seconds (2053.28 seconds total)