Starting phenix.real_space_refine (version: dev) on Mon Feb 20 03:48:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7au2_11923/02_2023/7au2_11923.pdb" } resolution = 2.43 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= 0.006 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 Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 728": "NH1" <-> "NH2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B GLU 763": "OE1" <-> "OE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 774": "NH1" <-> "NH2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B ARG 854": "NH1" <-> "NH2" Residue "B ARG 876": "NH1" <-> "NH2" Residue "B PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5540 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5540 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.59, per 1000 atoms: 0.59 Number of scatterers: 11236 At special positions: 0 Unit cell: (91.3379, 102.005, 103.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2042 8.00 N 1886 7.00 C 7252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.04 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " distance=2.04 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 41.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.688A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.841A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.889A pdb=" N GLY A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.922A pdb=" N ARG A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.687A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.500A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.840A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'B' and resid 522 through 538 Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.888A pdb=" N GLY B 641 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG B 728 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 Processing helix chain 'B' and resid 807 through 816 Processing helix chain 'B' and resid 818 through 829 removed outlier: 3.921A pdb=" N ARG B 822 " --> pdb=" O PRO B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR A 197 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU A 241 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 238 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 276 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 240 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 298 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE A 443 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU A 395 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 343 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU A 397 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 345 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR A 341 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA A 431 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE A 343 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE A 433 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE A 345 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 429 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 462 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 431 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 464 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 433 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 485 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 463 " --> pdb=" O VAL A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA A 551 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET A 716 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 692 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 718 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 694 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 663 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 664 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 743 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 666 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR B 197 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU B 241 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 238 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 276 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 240 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 298 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE B 443 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU B 395 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 343 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU B 397 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE B 345 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR B 341 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 431 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE B 343 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE B 433 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE B 345 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 429 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 462 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 431 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 464 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 433 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 485 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 463 " --> pdb=" O VAL B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA B 551 " --> pdb=" O ARG B 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 716 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 692 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 718 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 694 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 663 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 664 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 743 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL B 666 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 784 through 788 369 hydrogen bonds defined for protein. 957 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: 3.49 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3574 1.34 - 1.46: 2831 1.46 - 1.58: 5061 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 11554 Sorted by residual: bond pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N ILE B 829 " pdb=" CA ILE B 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" N ASN B 830 " pdb=" CA ASN B 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.95e+00 bond pdb=" N ASN A 830 " pdb=" CA ASN A 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.94e+00 bond pdb=" N PHE A 918 " pdb=" CA PHE A 918 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.38e-02 5.25e+03 5.24e+00 ... (remaining 11549 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.13: 376 106.13 - 113.10: 6128 113.10 - 120.07: 4096 120.07 - 127.04: 4943 127.04 - 134.01: 183 Bond angle restraints: 15726 Sorted by residual: angle pdb=" C ASN A 830 " pdb=" N CYS A 831 " pdb=" CA CYS A 831 " ideal model delta sigma weight residual 122.74 128.48 -5.74 1.44e+00 4.82e-01 1.59e+01 angle pdb=" C ASN B 830 " pdb=" N CYS B 831 " pdb=" CA CYS B 831 " ideal model delta sigma weight residual 122.74 128.40 -5.66 1.44e+00 4.82e-01 1.54e+01 angle pdb=" CA CYS A 831 " pdb=" C CYS A 831 " pdb=" O CYS A 831 " ideal model delta sigma weight residual 120.57 116.07 4.50 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA CYS B 831 " pdb=" C CYS B 831 " pdb=" O CYS B 831 " ideal model delta sigma weight residual 120.57 116.09 4.48 1.20e+00 6.94e-01 1.39e+01 angle pdb=" CA PRO A 583 " pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 15721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6288 17.99 - 35.97: 458 35.97 - 53.96: 100 53.96 - 71.94: 26 71.94 - 89.93: 28 Dihedral angle restraints: 6900 sinusoidal: 2862 harmonic: 4038 Sorted by residual: dihedral pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" N SER A 521 " pdb=" CA SER A 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N SER B 521 " pdb=" CA SER B 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL A 242 " pdb=" C VAL A 242 " pdb=" N GLY A 243 " pdb=" CA GLY A 243 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1695 0.105 - 0.210: 55 0.210 - 0.316: 0 0.316 - 0.421: 0 0.421 - 0.526: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB THR A 617 " pdb=" CA THR A 617 " pdb=" OG1 THR A 617 " pdb=" CG2 THR A 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB THR B 617 " pdb=" CA THR B 617 " pdb=" OG1 THR B 617 " pdb=" CG2 THR B 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA ILE B 829 " pdb=" N ILE B 829 " pdb=" C ILE B 829 " pdb=" CB ILE B 829 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 1749 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 582 " 0.041 5.00e-02 4.00e+02 5.96e-02 5.67e+00 pdb=" N PRO A 583 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 582 " -0.041 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO B 583 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 890 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 891 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 891 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 891 " 0.023 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 4300 2.89 - 3.40: 10155 3.40 - 3.90: 18642 3.90 - 4.40: 22307 4.40 - 4.90: 36722 Nonbonded interactions: 92126 Sorted by model distance: nonbonded pdb=" N ASP A 833 " pdb=" OD1 ASP A 833 " model vdw 2.392 2.520 nonbonded pdb=" N ASP B 833 " pdb=" OD1 ASP B 833 " model vdw 2.393 2.520 nonbonded pdb=" OE1 GLN B 819 " pdb=" NH1 ARG B 822 " model vdw 2.442 2.520 nonbonded pdb=" OE1 GLN A 819 " pdb=" NH1 ARG A 822 " model vdw 2.442 2.520 nonbonded pdb=" O VAL A 851 " pdb=" O VAL A 899 " model vdw 2.444 3.040 ... (remaining 92121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7252 2.51 5 N 1886 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 16.490 Check model and map are aligned: 0.180 Process input model: 30.980 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 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 : 0.005 0.086 11554 Z= 0.322 Angle : 0.675 6.040 15726 Z= 0.383 Chirality : 0.047 0.526 1752 Planarity : 0.005 0.060 2004 Dihedral : 14.843 89.928 4258 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.04 (0.22), residues: 1356 helix: 0.45 (0.25), residues: 438 sheet: -0.62 (0.38), residues: 172 loop : -0.04 (0.22), residues: 746 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.352 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 1.5025 time to fit residues: 221.9022 Evaluate side-chains 131 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1501 time to fit residues: 2.2072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 469 GLN A 616 HIS A 881 ASN B 216 GLN B 469 GLN B 616 HIS B 881 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11554 Z= 0.170 Angle : 0.543 5.842 15726 Z= 0.294 Chirality : 0.043 0.137 1752 Planarity : 0.005 0.046 2004 Dihedral : 4.897 21.203 1598 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.28 (0.22), residues: 1356 helix: 0.83 (0.25), residues: 464 sheet: -0.64 (0.38), residues: 172 loop : 0.09 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.360 Fit side-chains outliers start: 25 outliers final: 4 residues processed: 145 average time/residue: 1.4217 time to fit residues: 221.9210 Evaluate side-chains 129 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.9058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8613 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11554 Z= 0.245 Angle : 0.583 6.200 15726 Z= 0.316 Chirality : 0.045 0.146 1752 Planarity : 0.005 0.043 2004 Dihedral : 4.973 23.347 1598 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.35 (0.22), residues: 1356 helix: 1.03 (0.25), residues: 452 sheet: -0.70 (0.38), residues: 172 loop : 0.08 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.442 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 152 average time/residue: 1.4146 time to fit residues: 231.0383 Evaluate side-chains 149 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.1392 time to fit residues: 3.3035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 35 optimal weight: 0.0170 chunk 109 optimal weight: 10.0000 overall best weight: 2.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 782 HIS B 307 GLN B 782 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 11554 Z= 0.293 Angle : 0.612 6.949 15726 Z= 0.332 Chirality : 0.046 0.171 1752 Planarity : 0.006 0.052 2004 Dihedral : 5.116 24.715 1598 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.23 (0.22), residues: 1356 helix: 0.98 (0.25), residues: 452 sheet: -0.78 (0.39), residues: 168 loop : -0.03 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.245 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 155 average time/residue: 1.4876 time to fit residues: 246.9649 Evaluate side-chains 155 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.1343 time to fit residues: 3.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 874 HIS B 473 GLN B 874 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 11554 Z= 0.232 Angle : 0.567 6.318 15726 Z= 0.307 Chirality : 0.044 0.147 1752 Planarity : 0.005 0.049 2004 Dihedral : 4.950 23.496 1598 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.25 (0.22), residues: 1356 helix: 1.05 (0.25), residues: 452 sheet: -0.77 (0.39), residues: 168 loop : -0.06 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.263 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 153 average time/residue: 1.4779 time to fit residues: 242.7370 Evaluate side-chains 155 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.1271 time to fit residues: 3.3453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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: 0.8611 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11554 Z= 0.197 Angle : 0.544 5.944 15726 Z= 0.293 Chirality : 0.043 0.140 1752 Planarity : 0.005 0.045 2004 Dihedral : 4.812 22.400 1598 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.35 (0.22), residues: 1356 helix: 1.16 (0.25), residues: 452 sheet: -0.76 (0.39), residues: 168 loop : -0.01 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 155 average time/residue: 1.3843 time to fit residues: 230.7421 Evaluate side-chains 148 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.1456 time to fit residues: 2.4265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 11554 Z= 0.335 Angle : 0.641 6.898 15726 Z= 0.346 Chirality : 0.048 0.179 1752 Planarity : 0.006 0.054 2004 Dihedral : 5.163 25.330 1598 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.16 (0.22), residues: 1356 helix: 0.92 (0.25), residues: 452 sheet: -0.83 (0.39), residues: 168 loop : -0.08 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 152 average time/residue: 1.4564 time to fit residues: 237.5826 Evaluate side-chains 156 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.1170 time to fit residues: 3.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 11554 Z= 0.304 Angle : 0.619 6.798 15726 Z= 0.335 Chirality : 0.047 0.168 1752 Planarity : 0.006 0.053 2004 Dihedral : 5.131 24.930 1598 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.17 (0.22), residues: 1356 helix: 0.91 (0.25), residues: 452 sheet: -0.81 (0.39), residues: 168 loop : -0.06 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 153 average time/residue: 1.3975 time to fit residues: 229.4699 Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.1105 time to fit residues: 2.7235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 11554 Z= 0.157 Angle : 0.520 5.321 15726 Z= 0.279 Chirality : 0.042 0.135 1752 Planarity : 0.005 0.043 2004 Dihedral : 4.702 20.705 1598 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.45 (0.23), residues: 1356 helix: 1.27 (0.25), residues: 452 sheet: -0.72 (0.40), residues: 166 loop : 0.04 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 1.4470 time to fit residues: 229.3700 Evaluate side-chains 144 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 89 optimal weight: 0.0020 chunk 135 optimal weight: 0.0050 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 11554 Z= 0.246 Angle : 0.581 7.126 15726 Z= 0.313 Chirality : 0.045 0.144 1752 Planarity : 0.005 0.046 2004 Dihedral : 4.873 23.111 1598 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.36 (0.22), residues: 1356 helix: 1.14 (0.25), residues: 452 sheet: -0.72 (0.40), residues: 166 loop : 0.00 (0.22), residues: 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 147 average time/residue: 1.4855 time to fit residues: 234.3590 Evaluate side-chains 146 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.7502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.0050 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106616 restraints weight = 11228.556| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.72 r_work: 0.3026 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11554 Z= 0.178 Angle : 0.534 5.622 15726 Z= 0.286 Chirality : 0.043 0.136 1752 Planarity : 0.005 0.043 2004 Dihedral : 4.695 21.456 1598 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.45 (0.23), residues: 1356 helix: 1.26 (0.25), residues: 452 sheet: -0.70 (0.40), residues: 166 loop : 0.03 (0.22), residues: 738 =============================================================================== Job complete usr+sys time: 4315.90 seconds wall clock time: 77 minutes 38.13 seconds (4658.13 seconds total)