Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 16:21:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/04_2023/6wht_21675.pdb" } resolution = 4.39 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= 0.012 sd= 0.650 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 13142 2.51 5 N 3376 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20532 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 5250 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1265 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 44, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 4960 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 13, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 20, 'GLU:plan': 31, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 619 Chain: "C" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 5250 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1265 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 44, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 726 Chain: "D" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 4960 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 13, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 20, 'GLU:plan': 31, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 619 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: 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.93, per 1000 atoms: 0.53 Number of scatterers: 20532 At special positions: 0 Unit cell: (137, 152.07, 183.58, 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 74 16.00 O 3940 8.00 N 3376 7.00 C 13142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1003 " - " ASN A 224 " " NAG B 901 " - " ASN B 542 " " NAG C1003 " - " ASN C 224 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN A 389 " " NAG F 1 " - " ASN C 389 " Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 3.6 seconds 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 36 sheets defined 45.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.532A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.223A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.697A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 3.888A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.618A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.129A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.785A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.637A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.254A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.752A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 654 removed outlier: 4.672A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 742 No H-bonds generated for 'chain 'B' and resid 741 through 742' Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 772 through 785 Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 818 through 837 removed outlier: 3.705A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.531A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.224A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.696A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.889A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.619A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 861 " --> pdb=" O ALA C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 removed outlier: 4.128A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.784A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 341 removed outlier: 3.636A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 568 through 579 removed outlier: 4.253A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.751A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 654 removed outlier: 4.673A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 724 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 742 No H-bonds generated for 'chain 'D' and resid 741 through 742' Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 772 through 785 Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 818 through 837 removed outlier: 3.704A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.506A pdb=" N ILE A 240 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.161A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.295A pdb=" N LEU A 419 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 498 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA9, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 751 Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB6, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.524A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.582A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.507A pdb=" N ILE C 240 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.160A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.294A pdb=" N LEU C 419 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS C 498 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 431 through 434 Processing sheet with id=AC8, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AC9, first strand: chain 'C' and resid 555 through 557 Processing sheet with id=AD1, first strand: chain 'C' and resid 750 through 751 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AD5, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.523A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 765 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD8, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.581A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2790 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: 7.64 Time building geometry restraints manager: 9.25 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: 6723 1.34 - 1.46: 4937 1.46 - 1.58: 9156 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 20922 Sorted by residual: bond pdb=" C ALA A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.12e-02 7.97e+03 7.99e+00 bond pdb=" C ALA C 536 " pdb=" N PRO C 537 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.12e-02 7.97e+03 7.84e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" N GLY A 558 " pdb=" CA GLY A 558 " ideal model delta sigma weight residual 1.458 1.443 0.015 9.20e-03 1.18e+04 2.75e+00 ... (remaining 20917 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 533 106.38 - 113.29: 12360 113.29 - 120.21: 6996 120.21 - 127.13: 8770 127.13 - 134.04: 235 Bond angle restraints: 28894 Sorted by residual: angle pdb=" C SER D 526 " pdb=" N VAL D 527 " pdb=" CA VAL D 527 " ideal model delta sigma weight residual 122.59 119.55 3.04 7.20e-01 1.93e+00 1.78e+01 angle pdb=" C SER B 526 " pdb=" N VAL B 527 " pdb=" CA VAL B 527 " ideal model delta sigma weight residual 122.59 119.63 2.96 7.20e-01 1.93e+00 1.69e+01 angle pdb=" C SER A 464 " pdb=" CA SER A 464 " pdb=" CB SER A 464 " ideal model delta sigma weight residual 111.20 108.48 2.72 7.10e-01 1.98e+00 1.47e+01 angle pdb=" CA CYS D 321 " pdb=" CB CYS D 321 " pdb=" SG CYS D 321 " ideal model delta sigma weight residual 114.40 123.21 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA CYS B 321 " pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 28889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 11071 17.21 - 34.42: 821 34.42 - 51.62: 115 51.62 - 68.83: 33 68.83 - 86.04: 4 Dihedral angle restraints: 12044 sinusoidal: 3162 harmonic: 8882 Sorted by residual: dihedral pdb=" CA CYS B 321 " pdb=" C CYS B 321 " pdb=" N TYR B 322 " pdb=" CA TYR B 322 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.74e+01 dihedral pdb=" CA CYS D 321 " pdb=" C CYS D 321 " pdb=" N TYR D 322 " pdb=" CA TYR D 322 " ideal model delta harmonic sigma weight residual -180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA ARG B 439 " pdb=" C ARG B 439 " pdb=" N ILE B 440 " pdb=" CA ILE B 440 " ideal model delta harmonic sigma weight residual 180.00 131.15 48.85 0 5.00e+00 4.00e-02 9.54e+01 ... (remaining 12041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 3736 0.223 - 0.446: 2 0.446 - 0.669: 0 0.669 - 0.892: 0 0.892 - 1.114: 2 Chirality restraints: 3740 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.10e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" CB VAL C 756 " pdb=" CA VAL C 756 " pdb=" CG1 VAL C 756 " pdb=" CG2 VAL C 756 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3737 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 415 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 415 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 680 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.036 5.00e-02 4.00e+02 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 288 2.57 - 3.15: 21015 3.15 - 3.73: 32165 3.73 - 4.32: 40631 4.32 - 4.90: 60657 Nonbonded interactions: 154756 Sorted by model distance: nonbonded pdb=" OG1 THR C 446 " pdb=" O GLY C 449 " model vdw 1.983 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" O GLY A 449 " model vdw 1.983 2.440 nonbonded pdb=" OG SER B 170 " pdb=" O ILE B 227 " model vdw 2.004 2.440 nonbonded pdb=" OG SER D 170 " pdb=" O ILE D 227 " model vdw 2.005 2.440 nonbonded pdb=" OG SER D 34 " pdb=" O VAL D 65 " model vdw 2.047 2.440 ... (remaining 154751 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' 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: 1.370 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: 6.390 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 54.530 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.006 0.053 20922 Z= 0.429 Angle : 0.852 10.387 28894 Z= 0.485 Chirality : 0.053 1.114 3740 Planarity : 0.006 0.073 3682 Dihedral : 12.853 86.039 6244 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 17.34 % Favored : 82.33 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.12), residues: 3034 helix: -2.83 (0.12), residues: 1140 sheet: -3.98 (0.24), residues: 284 loop : -3.89 (0.14), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.2307 time to fit residues: 81.4248 Evaluate side-chains 159 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 2.441 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1764 time to fit residues: 5.1239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 40.0000 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 0.0670 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 147 GLN B 118 GLN B 159 ASN B 184 ASN B 486 HIS B 615 ASN B 616 ASN C 50 ASN C 147 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 184 ASN D 486 HIS D 616 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20922 Z= 0.200 Angle : 0.687 12.664 28894 Z= 0.363 Chirality : 0.046 0.259 3740 Planarity : 0.005 0.069 3682 Dihedral : 6.361 45.998 3144 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.22 % Favored : 89.52 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.48 (0.14), residues: 3034 helix: -1.03 (0.13), residues: 1226 sheet: -3.31 (0.23), residues: 330 loop : -3.27 (0.15), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 227 average time/residue: 0.2432 time to fit residues: 96.3579 Evaluate side-chains 171 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1763 time to fit residues: 3.7438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 801 HIS D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20922 Z= 0.253 Angle : 0.690 13.067 28894 Z= 0.365 Chirality : 0.045 0.235 3740 Planarity : 0.005 0.062 3682 Dihedral : 6.246 48.955 3144 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.23 % Favored : 87.64 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.86 (0.15), residues: 3034 helix: -0.35 (0.14), residues: 1234 sheet: -3.06 (0.24), residues: 328 loop : -3.07 (0.16), residues: 1472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 193 average time/residue: 0.2251 time to fit residues: 78.7757 Evaluate side-chains 158 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1732 time to fit residues: 3.8556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 10.0000 chunk 209 optimal weight: 0.0670 chunk 144 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 264 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN D 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20922 Z= 0.258 Angle : 0.678 12.974 28894 Z= 0.359 Chirality : 0.045 0.239 3740 Planarity : 0.005 0.065 3682 Dihedral : 6.188 46.047 3144 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.96 % Favored : 87.90 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.53 (0.15), residues: 3034 helix: 0.01 (0.15), residues: 1234 sheet: -2.91 (0.25), residues: 330 loop : -2.97 (0.16), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 195 average time/residue: 0.2806 time to fit residues: 97.1343 Evaluate side-chains 157 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2105 time to fit residues: 3.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 0.0000 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 392 HIS A 637 ASN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN C 134 HIS C 392 HIS ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 20922 Z= 0.183 Angle : 0.632 13.247 28894 Z= 0.330 Chirality : 0.044 0.256 3740 Planarity : 0.005 0.063 3682 Dihedral : 5.849 50.619 3144 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.84 % Favored : 89.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.07 (0.15), residues: 3034 helix: 0.44 (0.15), residues: 1226 sheet: -2.55 (0.27), residues: 308 loop : -2.79 (0.16), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2407 time to fit residues: 83.0542 Evaluate side-chains 160 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.0970 chunk 266 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 336 ASN D 649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20922 Z= 0.249 Angle : 0.658 13.433 28894 Z= 0.346 Chirality : 0.045 0.280 3740 Planarity : 0.005 0.062 3682 Dihedral : 5.851 46.287 3144 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.80 % Favored : 88.07 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 3034 helix: 0.49 (0.15), residues: 1222 sheet: -2.63 (0.26), residues: 324 loop : -2.72 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2367 time to fit residues: 79.5508 Evaluate side-chains 155 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20922 Z= 0.239 Angle : 0.658 13.236 28894 Z= 0.345 Chirality : 0.045 0.352 3740 Planarity : 0.005 0.063 3682 Dihedral : 5.834 49.662 3144 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.21 % Favored : 88.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.92 (0.16), residues: 3034 helix: 0.59 (0.15), residues: 1222 sheet: -2.64 (0.27), residues: 300 loop : -2.67 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2386 time to fit residues: 76.8058 Evaluate side-chains 157 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 717 GLN D 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 20922 Z= 0.251 Angle : 0.662 13.554 28894 Z= 0.346 Chirality : 0.045 0.269 3740 Planarity : 0.005 0.062 3682 Dihedral : 5.831 50.659 3144 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.80 % Favored : 88.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.87 (0.16), residues: 3034 helix: 0.61 (0.15), residues: 1222 sheet: -2.62 (0.27), residues: 300 loop : -2.61 (0.16), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2395 time to fit residues: 79.1988 Evaluate side-chains 156 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 274 optimal weight: 40.0000 chunk 165 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20922 Z= 0.270 Angle : 0.683 13.835 28894 Z= 0.357 Chirality : 0.046 0.437 3740 Planarity : 0.005 0.063 3682 Dihedral : 5.877 48.883 3144 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.06 % Favored : 87.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.98 (0.16), residues: 3034 helix: 0.49 (0.15), residues: 1230 sheet: -2.65 (0.27), residues: 314 loop : -2.66 (0.16), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2377 time to fit residues: 75.9352 Evaluate side-chains 154 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.299 > 50: distance: 17 - 23: 31.542 distance: 23 - 24: 12.884 distance: 24 - 25: 42.563 distance: 25 - 26: 45.503 distance: 25 - 27: 36.410 distance: 27 - 28: 12.828 distance: 28 - 29: 39.239 distance: 28 - 31: 40.666 distance: 29 - 30: 22.115 distance: 29 - 36: 19.457 distance: 31 - 32: 23.185 distance: 32 - 33: 31.287 distance: 33 - 34: 30.348 distance: 34 - 35: 39.938 distance: 36 - 37: 16.495 distance: 37 - 38: 18.708 distance: 37 - 40: 37.118 distance: 38 - 39: 30.312 distance: 38 - 44: 16.601 distance: 40 - 41: 17.719 distance: 41 - 42: 45.887 distance: 41 - 43: 43.269 distance: 44 - 45: 35.642 distance: 45 - 46: 42.032 distance: 45 - 48: 32.754 distance: 46 - 47: 49.260 distance: 46 - 49: 23.075 distance: 47 - 70: 40.933 distance: 49 - 50: 40.752 distance: 50 - 51: 42.240 distance: 50 - 53: 42.128 distance: 51 - 52: 25.131 distance: 51 - 55: 12.555 distance: 53 - 54: 30.817 distance: 55 - 56: 22.789 distance: 56 - 57: 6.203 distance: 56 - 59: 23.977 distance: 57 - 58: 21.088 distance: 57 - 60: 18.565 distance: 58 - 84: 43.311 distance: 60 - 61: 15.544 distance: 61 - 62: 13.500 distance: 61 - 64: 10.216 distance: 62 - 63: 20.523 distance: 62 - 70: 21.899 distance: 63 - 92: 24.088 distance: 64 - 65: 30.951 distance: 65 - 66: 12.516 distance: 65 - 67: 16.838 distance: 66 - 68: 16.138 distance: 67 - 69: 14.673 distance: 68 - 69: 19.172 distance: 70 - 71: 23.417 distance: 71 - 72: 27.116 distance: 71 - 74: 27.377 distance: 72 - 73: 50.424 distance: 72 - 78: 47.027 distance: 73 - 97: 33.216 distance: 74 - 75: 51.457 distance: 74 - 76: 24.780 distance: 75 - 77: 26.532 distance: 78 - 79: 23.389 distance: 79 - 80: 36.460 distance: 79 - 82: 31.986 distance: 80 - 81: 29.429 distance: 80 - 84: 10.678 distance: 81 - 104: 22.933 distance: 82 - 83: 22.489 distance: 84 - 85: 11.500 distance: 85 - 86: 6.505 distance: 85 - 88: 29.791 distance: 86 - 87: 30.858 distance: 86 - 92: 21.596 distance: 87 - 108: 21.478 distance: 88 - 89: 44.076 distance: 89 - 90: 27.175 distance: 89 - 91: 43.434